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HEADER HYDROLASE 14-MAR-12 4AN1
TITLE PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND
TITLE 2 INHIBITOR IC-4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROLYL ENDOPEPTIDASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PE, POST-PROLINE CLEAVING ENZYME;
COMPND 5 EC: 3.4.21.26;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA;
SOURCE 3 ORGANISM_COMMON: PIG;
SOURCE 4 ORGANISM_TAXID: 9823;
SOURCE 5 ORGAN: BRAIN;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM105
KEYWDS ALPHA/BETA-HYDROLASE, AMNESIA, BETA-PROPELLER, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.KASZUBA,T.ROG,R.DANNE,P.CANNING,V.FULOP,T.JUHASZ,Z.SZELTNER,
AUTHOR 2 J.F.ST- PIERRE,A.GARCIA-HORSMAN,P.T.MANNISTO,M.KARTTUNEN,J.HOKKANEN,
AUTHOR 3 A.BUNKER
REVDAT 1 16-MAY-12 4AN1 0
JRNL AUTH K.KASZUBA,T.ROG,R.DANNE,P.CANNING,V.FULOP,T.JUHASZ,
JRNL AUTH 2 Z.SZELTNER,J.F.ST-PIERRE,A.GARCIA-HORSMAN,P.T.MANNISTO,
JRNL AUTH 3 M.KARTTUNEN,J.HOKKANEN,A.BUNKER
JRNL TITL MOLECULAR DYNAMICS, CRYSTALLOGRAPHY AND MUTAGENESIS STUDIES
JRNL TITL 2 ON THE SUBSTRATE GATING MECHANISM OF PROLYL OLIGOPEPTIDASE.
JRNL REF BIOCHIMIE V. 94 1398 2012
JRNL REFN ISSN 0300-9084
JRNL PMID 22484394
JRNL DOI 10.1016/J.BIOCHI.2012.03.012
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.33
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.26
REMARK 3 NUMBER OF REFLECTIONS : 54481
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.16970
REMARK 3 R VALUE (WORKING SET) : 0.16772
REMARK 3 FREE R VALUE : 0.21452
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.1
REMARK 3 FREE R VALUE TEST SET COUNT : 2341
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.901
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.950
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3932
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.10
REMARK 3 BIN R VALUE (WORKING SET) : 0.218
REMARK 3 BIN FREE R VALUE SET COUNT : 149
REMARK 3 BIN FREE R VALUE : 0.261
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5701
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 50
REMARK 3 SOLVENT ATOMS : 611
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.7
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.370
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.63
REMARK 3 B22 (A**2) : -0.63
REMARK 3 B33 (A**2) : 1.27
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.155
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.747
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5904 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7999 ; 1.474 ; 1.956
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 709 ; 6.448 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 285 ;33.676 ;24.316
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 972 ;13.144 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;19.805 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 844 ; 0.107 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4539 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3524 ; 0.821 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5690 ; 1.484 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2380 ; 2.558 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2309 ; 4.027 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 72
REMARK 3 ORIGIN FOR THE GROUP (A): 35.0380 49.5560 66.3520
REMARK 3 T TENSOR
REMARK 3 T11: 0.1977 T22: 0.1061
REMARK 3 T33: 0.1284 T12: -0.0004
REMARK 3 T13: 0.0086 T23: 0.0146
REMARK 3 L TENSOR
REMARK 3 L11: 0.6047 L22: 0.1289
REMARK 3 L33: 0.7092 L12: -0.0375
REMARK 3 L13: -0.4512 L23: 0.1041
REMARK 3 S TENSOR
REMARK 3 S11: -0.0222 S12: 0.0023 S13: 0.0681
REMARK 3 S21: -0.0808 S22: 0.0231 S23: 0.0076
REMARK 3 S31: -0.0267 S32: 0.0234 S33: -0.0010
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 73 A 427
REMARK 3 ORIGIN FOR THE GROUP (A): 43.2650 41.0040 102.3430
REMARK 3 T TENSOR
REMARK 3 T11: 0.1855 T22: 0.1397
REMARK 3 T33: 0.1131 T12: 0.0069
REMARK 3 T13: -0.0002 T23: -0.0096
REMARK 3 L TENSOR
REMARK 3 L11: 0.1501 L22: 0.2474
REMARK 3 L33: 0.1295 L12: 0.0018
REMARK 3 L13: -0.0047 L23: -0.0511
REMARK 3 S TENSOR
REMARK 3 S11: -0.0036 S12: -0.0228 S13: 0.0048
REMARK 3 S21: 0.0414 S22: 0.0076 S23: -0.0077
REMARK 3 S31: -0.0132 S32: 0.0040 S33: -0.0039
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 428 A 710
REMARK 3 ORIGIN FOR THE GROUP (A): 26.0500 39.5950 76.7130
REMARK 3 T TENSOR
REMARK 3 T11: 0.1701 T22: 0.1353
REMARK 3 T33: 0.1300 T12: 0.0023
REMARK 3 T13: -0.0035 T23: 0.0004
REMARK 3 L TENSOR
REMARK 3 L11: 0.1554 L22: 0.2978
REMARK 3 L33: 0.2071 L12: -0.0211
REMARK 3 L13: -0.0952 L23: -0.0856
REMARK 3 S TENSOR
REMARK 3 S11: -0.0189 S12: -0.0086 S13: 0.0060
REMARK 3 S21: -0.0343 S22: 0.0191 S23: 0.0192
REMARK 3 S31: -0.0003 S32: -0.0197 S33: -0.0003
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 791 A 791
REMARK 3 ORIGIN FOR THE GROUP (A): 41.4640 37.2580 85.4190
REMARK 3 T TENSOR
REMARK 3 T11: 0.1674 T22: 0.2080
REMARK 3 T33: 0.2482 T12: -0.1030
REMARK 3 T13: -0.0568 T23: 0.1019
REMARK 3 L TENSOR
REMARK 3 L11: 20.2607 L22: 1.6350
REMARK 3 L33: 48.2865 L12: -4.7633
REMARK 3 L13: 26.7065 L23: -3.6831
REMARK 3 S TENSOR
REMARK 3 S11: 0.2792 S12: -0.5876 S13: -0.7522
REMARK 3 S21: -0.2267 S22: 0.2760 S23: 0.2742
REMARK 3 S31: -0.3714 S32: 0.0497 S33: -0.5553
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK 3 RIDING POSITIONS. U VALUES RESIDUAL ONLY
REMARK 4
REMARK 4 4AN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-12.
REMARK 100 THE PDBE ID CODE IS EBI-51699.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-MAR-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9756
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315R)
REMARK 200 DETECTOR MANUFACTURER : ADSC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56822
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90
REMARK 200 RESOLUTION RANGE LOW (A) : 75.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5
REMARK 200 DATA REDUNDANCY : 3.5
REMARK 200 R MERGE (I) : 0.09
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 13.10
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7
REMARK 200 DATA REDUNDANCY IN SHELL : 3.6
REMARK 200 R MERGE FOR SHELL (I) : 0.56
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 2.00
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 1QFS
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.5
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% METHOXY-POLYETHYLENE GLYCOL
REMARK 280 (MPEG) 5K, 20 MM CA(OAC)2, 0.1 M TRIS PH 8.5, 15% GLYCEROL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.25000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.70000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.50000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.70000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.25000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.50000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O TYR A 292 O2 GOL A 1715 2.13
REMARK 500 O HOH A 2088 O HOH A 2211 2.19
REMARK 500 O HOH A 2241 O HOH A 2242 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 LEU A 351 CB - CG - CD2 ANGL. DEV. = 11.2 DEGREES
REMARK 500 ARG A 702 CG - CD - NE ANGL. DEV. = -14.3 DEGREES
REMARK 500 ARG A 702 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 3 31.66 -86.30
REMARK 500 ASN A 271 45.42 -156.38
REMARK 500 HIS A 307 18.20 57.60
REMARK 500 TYR A 311 151.22 75.42
REMARK 500 ASP A 320 63.68 -151.72
REMARK 500 LYS A 335 -33.77 -134.96
REMARK 500 SER A 346 -56.08 72.99
REMARK 500 ASP A 356 47.95 39.36
REMARK 500 TYR A 473 -75.31 -123.44
REMARK 500 LEU A 520 -125.56 63.27
REMARK 500 SER A 554 -115.58 72.06
REMARK 500 THR A 590 -112.10 30.26
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 1-[(2R,5S)-2-TERT-BUTYL-5-({(2S)-2-[(1R)-1,2-
REMARK 600 DIHYDROXYETHYL]PYRROLIDIN-1-YL}CARBONYL)PYRROLIDIN-1-YL]-4-
REMARK 600 PHENYLBUTAN-1-ONE (178): COVALENTLY BOUND TO SER554
REMARK 630
REMARK 630 MOLECULE TYPE: INHIBITOR
REMARK 630 MOLECULE NAME: 1-[(2R,5S)-2-TERT-BUTYL-5-({(2S)-2-[(1R)-1,2-
REMARK 630 DIHYDROXYETHYL]PYRROLIDIN-1-YL}CARBONYL)PYRROLIDIN-1-YL]-4-
REMARK 630 PHENYLBUTAN-1-ONE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 2P8 A 791
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: PMQ PRO TPK
REMARK 630 DETAILS: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2P8 A 791
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1712
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1713
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1714
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1715
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1E5T RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT
REMARK 900 RELATED ID: 1E8M RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT,
REMARK 900 COMPLEXED WITH INHIBITOR
REMARK 900 RELATED ID: 1E8N RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT,
REMARK 900 COMPLEXED WITH PEPTIDE
REMARK 900 RELATED ID: 1H2W RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN
REMARK 900 RELATED ID: 1H2X RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT
REMARK 900 RELATED ID: 1H2Y RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT
REMARK 900 WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
REMARK 900 RELATED ID: 1H2Z RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
REMARK 900 RELATED ID: 1O6F RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641A MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
REMARK 900 RELATED ID: 1O6G RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641N MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
REMARK 900 RELATED ID: 1QFM RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE
REMARK 900 RELATED ID: 1QFS RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY
REMARK 900 BOUND INHIBITOR Z-PRO-PROLINAL
REMARK 900 RELATED ID: 1UOO RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND GLY-PHE-ARG-PRO
REMARK 900 RELATED ID: 1UOP RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND GLY-PHE-GLU-PRO
REMARK 900 RELATED ID: 1UOQ RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT
REMARK 900 WITH BOUND PEPTIDE LIGAND GLU-PHE-SER-PRO
REMARK 900 RELATED ID: 1VZ2 RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y73C/V427C/
REMARK 900 C255T MUTANT
REMARK 900 RELATED ID: 1VZ3 RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, T597C MUTANT
REMARK 900 RELATED ID: 2XDW RELATED DB: PDB
REMARK 900 INHIBITION OF PROLYL OLIGOPEPTIDASE WITH A SYNTHETIC
REMARK 900 UNNATURAL DIPEPTIDE
REMARK 900 RELATED ID: 4AMY RELATED DB: PDB
REMARK 900 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A
REMARK 900 COVALENTLY BOUND INHIBITOR IC-1
DBREF 4AN1 A 1 710 UNP P23687 PPCE_PIG 1 710
SEQRES 1 A 710 MET LEU SER PHE GLN TYR PRO ASP VAL TYR ARG ASP GLU
SEQRES 2 A 710 THR ALA ILE GLN ASP TYR HIS GLY HIS LYS VAL CYS ASP
SEQRES 3 A 710 PRO TYR ALA TRP LEU GLU ASP PRO ASP SER GLU GLN THR
SEQRES 4 A 710 LYS ALA PHE VAL GLU ALA GLN ASN LYS ILE THR VAL PRO
SEQRES 5 A 710 PHE LEU GLU GLN CYS PRO ILE ARG GLY LEU TYR LYS GLU
SEQRES 6 A 710 ARG MET THR GLU LEU TYR ASP TYR PRO LYS TYR SER CYS
SEQRES 7 A 710 HIS PHE LYS LYS GLY LYS ARG TYR PHE TYR PHE TYR ASN
SEQRES 8 A 710 THR GLY LEU GLN ASN GLN ARG VAL LEU TYR VAL GLN ASP
SEQRES 9 A 710 SER LEU GLU GLY GLU ALA ARG VAL PHE LEU ASP PRO ASN
SEQRES 10 A 710 ILE LEU SER ASP ASP GLY THR VAL ALA LEU ARG GLY TYR
SEQRES 11 A 710 ALA PHE SER GLU ASP GLY GLU TYR PHE ALA TYR GLY LEU
SEQRES 12 A 710 SER ALA SER GLY SER ASP TRP VAL THR ILE LYS PHE MET
SEQRES 13 A 710 LYS VAL ASP GLY ALA LYS GLU LEU PRO ASP VAL LEU GLU
SEQRES 14 A 710 ARG VAL LYS PHE SER CYS MET ALA TRP THR HIS ASP GLY
SEQRES 15 A 710 LYS GLY MET PHE TYR ASN ALA TYR PRO GLN GLN ASP GLY
SEQRES 16 A 710 LYS SER ASP GLY THR GLU THR SER THR ASN LEU HIS GLN
SEQRES 17 A 710 LYS LEU TYR TYR HIS VAL LEU GLY THR ASP GLN SER GLU
SEQRES 18 A 710 ASP ILE LEU CYS ALA GLU PHE PRO ASP GLU PRO LYS TRP
SEQRES 19 A 710 MET GLY GLY ALA GLU LEU SER ASP ASP GLY ARG TYR VAL
SEQRES 20 A 710 LEU LEU SER ILE ARG GLU GLY CYS ASP PRO VAL ASN ARG
SEQRES 21 A 710 LEU TRP TYR CYS ASP LEU GLN GLN GLU SER ASN GLY ILE
SEQRES 22 A 710 THR GLY ILE LEU LYS TRP VAL LYS LEU ILE ASP ASN PHE
SEQRES 23 A 710 GLU GLY GLU TYR ASP TYR VAL THR ASN GLU GLY THR VAL
SEQRES 24 A 710 PHE THR PHE LYS THR ASN ARG HIS SER PRO ASN TYR ARG
SEQRES 25 A 710 LEU ILE ASN ILE ASP PHE THR ASP PRO GLU GLU SER LYS
SEQRES 26 A 710 TRP LYS VAL LEU VAL PRO GLU HIS GLU LYS ASP VAL LEU
SEQRES 27 A 710 GLU TRP VAL ALA CYS VAL ARG SER ASN PHE LEU VAL LEU
SEQRES 28 A 710 CYS TYR LEU HIS ASP VAL LYS ASN THR LEU GLN LEU HIS
SEQRES 29 A 710 ASP LEU ALA THR GLY ALA LEU LEU LYS ILE PHE PRO LEU
SEQRES 30 A 710 GLU VAL GLY SER VAL VAL GLY TYR SER GLY GLN LYS LYS
SEQRES 31 A 710 ASP THR GLU ILE PHE TYR GLN PHE THR SER PHE LEU SER
SEQRES 32 A 710 PRO GLY ILE ILE TYR HIS CYS ASP LEU THR LYS GLU GLU
SEQRES 33 A 710 LEU GLU PRO ARG VAL PHE ARG GLU VAL THR VAL LYS GLY
SEQRES 34 A 710 ILE ASP ALA SER ASP TYR GLN THR VAL GLN ILE PHE TYR
SEQRES 35 A 710 PRO SER LYS ASP GLY THR LYS ILE PRO MET PHE ILE VAL
SEQRES 36 A 710 HIS LYS LYS GLY ILE LYS LEU ASP GLY SER HIS PRO ALA
SEQRES 37 A 710 PHE LEU TYR GLY TYR GLY GLY PHE ASN ILE SER ILE THR
SEQRES 38 A 710 PRO ASN TYR SER VAL SER ARG LEU ILE PHE VAL ARG HIS
SEQRES 39 A 710 MET GLY GLY VAL LEU ALA VAL ALA ASN ILE ARG GLY GLY
SEQRES 40 A 710 GLY GLU TYR GLY GLU THR TRP HIS LYS GLY GLY ILE LEU
SEQRES 41 A 710 ALA ASN LYS GLN ASN CYS PHE ASP ASP PHE GLN CYS ALA
SEQRES 42 A 710 ALA GLU TYR LEU ILE LYS GLU GLY TYR THR SER PRO LYS
SEQRES 43 A 710 ARG LEU THR ILE ASN GLY GLY SER ASN GLY GLY LEU LEU
SEQRES 44 A 710 VAL ALA THR CYS ALA ASN GLN ARG PRO ASP LEU PHE GLY
SEQRES 45 A 710 CYS VAL ILE ALA GLN VAL GLY VAL MET ASP MET LEU LYS
SEQRES 46 A 710 PHE HIS LYS TYR THR ILE GLY HIS ALA TRP THR THR ASP
SEQRES 47 A 710 TYR GLY CYS SER ASP SER LYS GLN HIS PHE GLU TRP LEU
SEQRES 48 A 710 ILE LYS TYR SER PRO LEU HIS ASN VAL LYS LEU PRO GLU
SEQRES 49 A 710 ALA ASP ASP ILE GLN TYR PRO SER MET LEU LEU LEU THR
SEQRES 50 A 710 ALA ASP HIS ASP ASP ARG VAL VAL PRO LEU HIS SER LEU
SEQRES 51 A 710 LYS PHE ILE ALA THR LEU GLN TYR ILE VAL GLY ARG SER
SEQRES 52 A 710 ARG LYS GLN ASN ASN PRO LEU LEU ILE HIS VAL ASP THR
SEQRES 53 A 710 LYS ALA GLY HIS GLY ALA GLY LYS PRO THR ALA LYS VAL
SEQRES 54 A 710 ILE GLU GLU VAL SER ASP MET PHE ALA PHE ILE ALA ARG
SEQRES 55 A 710 CYS LEU ASN ILE ASP TRP ILE PRO
HET 2P8 A 791 26
HET GOL A1712 6
HET GOL A1713 6
HET GOL A1714 6
HET GOL A1715 6
HETNAM 2P8 (2S)-N-BENZYL-2-({(2S)-2-[(1R)-1,2-
HETNAM 2 2P8 DIHYDROXYETHYL]PYRROLIDIN-1-YL}CARBONYL)PYRROLIDINE-1-
HETNAM 3 2P8 CARBOXAMIDE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 2P8 C19 H27 N3 O4
FORMUL 3 GOL 4(C3 H8 O3)
FORMUL 4 HOH *611(H2 O)
HELIX 1 1 TYR A 28 ASP A 33 5 6
HELIX 2 2 SER A 36 GLN A 56 1 21
HELIX 3 3 CYS A 57 TYR A 71 1 15
HELIX 4 4 ASP A 115 SER A 120 5 6
HELIX 5 5 ASP A 218 ASP A 222 5 5
HELIX 6 6 GLN A 267 GLU A 269 5 3
HELIX 7 7 GLU A 322 TRP A 326 5 5
HELIX 8 8 ASP A 431 SER A 433 5 3
HELIX 9 9 SER A 485 GLY A 496 1 12
HELIX 10 10 TYR A 510 GLY A 517 1 8
HELIX 11 11 GLY A 518 ASN A 522 5 5
HELIX 12 12 LYS A 523 GLU A 540 1 18
HELIX 13 13 SER A 544 LYS A 546 5 3
HELIX 14 14 SER A 554 ARG A 567 1 14
HELIX 15 15 PRO A 568 PHE A 571 5 4
HELIX 16 16 LYS A 585 TYR A 589 5 5
HELIX 17 17 ILE A 591 ALA A 594 5 4
HELIX 18 18 TRP A 595 GLY A 600 1 6
HELIX 19 19 SER A 604 ILE A 612 1 9
HELIX 20 20 SER A 615 ASN A 619 5 5
HELIX 21 21 PRO A 646 VAL A 660 1 15
HELIX 22 22 PRO A 685 ASN A 705 1 21
SHEET 1 AA 2 ILE A 16 TYR A 19 0
SHEET 2 AA 2 HIS A 22 CYS A 25 -1 O HIS A 22 N TYR A 19
SHEET 1 AB 2 LYS A 75 TYR A 76 0
SHEET 2 AB 2 ARG A 85 ASN A 91 -1 O ASN A 91 N LYS A 75
SHEET 1 AC 2 PHE A 80 LYS A 82 0
SHEET 2 AC 2 ARG A 85 ASN A 91 -1 O ARG A 85 N LYS A 82
SHEET 1 AD 4 ARG A 111 LEU A 114 0
SHEET 2 AD 4 VAL A 99 GLN A 103 -1 O LEU A 100 N PHE A 113
SHEET 3 AD 4 ARG A 85 ASN A 91 -1 O TYR A 86 N GLN A 103
SHEET 4 AD 4 PHE A 80 LYS A 82 -1 O PHE A 80 N PHE A 87
SHEET 1 AE 4 ARG A 111 LEU A 114 0
SHEET 2 AE 4 VAL A 99 GLN A 103 -1 O LEU A 100 N PHE A 113
SHEET 3 AE 4 ARG A 85 ASN A 91 -1 O TYR A 86 N GLN A 103
SHEET 4 AE 4 LYS A 75 TYR A 76 -1 O LYS A 75 N ASN A 91
SHEET 1 AF 7 VAL A 125 PHE A 132 0
SHEET 2 AF 7 TYR A 138 ALA A 145 -1 O ALA A 140 N ALA A 131
SHEET 3 AF 7 VAL A 151 LYS A 157 -1 O THR A 152 N LEU A 143
SHEET 4 AF 7 LYS A 162 TRP A 178 -1 O LYS A 162 N LYS A 157
SHEET 5 AF 7 GLY A 184 ALA A 189 -1 O PHE A 186 N ALA A 177
SHEET 6 AF 7 LYS A 209 VAL A 214 -1 O LYS A 209 N ALA A 189
SHEET 7 AF 7 ILE A 223 ALA A 226 -1 O ILE A 223 N TYR A 212
SHEET 1 AG 4 MET A 235 LEU A 240 0
SHEET 2 AG 4 TYR A 246 ARG A 252 -1 O LEU A 248 N GLU A 239
SHEET 3 AG 4 ARG A 260 ASP A 265 -1 O ARG A 260 N ILE A 251
SHEET 4 AG 4 VAL A 280 ILE A 283 -1 O VAL A 280 N TYR A 263
SHEET 1 AH 4 TYR A 290 GLU A 296 0
SHEET 2 AH 4 VAL A 299 THR A 304 -1 O VAL A 299 N GLU A 296
SHEET 3 AH 4 ARG A 312 ASP A 317 -1 O ARG A 312 N THR A 304
SHEET 4 AH 4 LYS A 327 VAL A 330 -1 O LYS A 327 N ASN A 315
SHEET 1 AI 4 VAL A 337 VAL A 344 0
SHEET 2 AI 4 PHE A 348 HIS A 355 -1 O PHE A 348 N VAL A 344
SHEET 3 AI 4 LYS A 358 ASP A 365 -1 O LYS A 358 N HIS A 355
SHEET 4 AI 4 LEU A 371 PHE A 375 -1 N LEU A 372 O LEU A 363
SHEET 1 AJ 4 SER A 381 SER A 386 0
SHEET 2 AJ 4 GLU A 393 THR A 399 -1 O PHE A 395 N SER A 386
SHEET 3 AJ 4 ILE A 406 ASP A 411 -1 O ILE A 406 N PHE A 398
SHEET 4 AJ 4 ARG A 420 GLU A 424 -1 O ARG A 420 N HIS A 409
SHEET 1 AK 8 TYR A 435 PRO A 443 0
SHEET 2 AK 8 LYS A 449 LYS A 457 -1 O ILE A 450 N TYR A 442
SHEET 3 AK 8 VAL A 498 ALA A 502 -1 O LEU A 499 N VAL A 455
SHEET 4 AK 8 ALA A 468 TYR A 471 1 O PHE A 469 N ALA A 500
SHEET 5 AK 8 LEU A 548 GLY A 553 1 O THR A 549 N LEU A 470
SHEET 6 AK 8 CYS A 573 GLN A 577 1 O CYS A 573 N ILE A 550
SHEET 7 AK 8 SER A 632 ALA A 638 1 O SER A 632 N VAL A 574
SHEET 8 AK 8 LEU A 670 ASP A 675 1 O LEU A 671 N LEU A 635
LINK C1 2P8 A 791 OG SER A 554 1555 1555 1.38
SITE 1 AC1 13 PHE A 173 MET A 235 TYR A 473 PHE A 476
SITE 2 AC1 13 SER A 554 ASN A 555 VAL A 580 TRP A 595
SITE 3 AC1 13 TYR A 599 ARG A 643 VAL A 644 HIS A 680
SITE 4 AC1 13 HOH A2609
SITE 1 AC2 9 ILE A 118 LEU A 119 SER A 120 ASP A 121
SITE 2 AC2 9 ASP A 446 ASN A 525 HOH A2496 HOH A2498
SITE 3 AC2 9 HOH A2610
SITE 1 AC3 7 ALA A 226 GLU A 227 PHE A 228 TRP A 262
SITE 2 AC3 7 ILE A 276 LYS A 281 HOH A2611
SITE 1 AC4 10 PRO A 568 ASP A 569 PHE A 571 GLY A 572
SITE 2 AC4 10 ILE A 628 GLN A 629 PRO A 631 ASN A 668
SITE 3 AC4 10 HOH A2513 HOH A2578
SITE 1 AC5 5 GLU A 239 ASP A 291 TYR A 292 HOH A2298
SITE 2 AC5 5 HOH A2356
CRYST1 70.500 99.000 109.400 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.014184 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010101 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009141 0.00000
TER 5702 PRO A 710
MASTER 453 0 5 22 45 0 14 6 6362 1 51 55
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