| content |
HEADER HYDROLASE 09-APR-20 6WIA
TITLE CRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-
TITLE 2 INHIBITED (AGED)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOSOMAL PROTECTIVE PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CARBOXYPEPTIDASE C,CARBOXYPEPTIDASE L,CATHEPSIN A,PROTECTIVE
COMPND 5 PROTEIN CATHEPSIN A,PPCA,PROTECTIVE PROTEIN FOR BETA-GALACTOSIDASE;
COMPND 6 EC: 3.4.16.5;
COMPND 7 ENGINEERED: YES;
COMPND 8 OTHER_DETAILS: ZYMOGEN ACTIVATED BY CATHEPSIN L
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: CTSA, PPGB;
SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: EXPI293;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCDNA3.4
KEYWDS LYSOSOMAL, CATHEPSIN A, CATA, CTSA, ORGANOPHOSPHATE, RENIN-
KEYWDS 2 ANGIOTENSIN SYSTEM (RAS), HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.COMPTON,P.M.LEGLER
REVDAT 1 29-APR-20 6WIA 0
JRNL AUTH K.D.BOUKNIGHT,K.M.JURKOUICH,J.R.COMPTON,I.V.KHAVRUTSKII,
JRNL AUTH 2 M.A.GUELTA,S.P.HARVEY,P.M.LEGLER
JRNL TITL STRUCTURAL AND KINETIC EVIDENCE OF AGING AFTER
JRNL TITL 2 ORGANOPHOSPHATE INHIBITION OF HUMAN CATHEPSIN A.
JRNL REF BIOCHEM. PHARMACOL. 13980 2020
JRNL REFN ISSN 1873-2968
JRNL PMID 32305437
JRNL DOI 10.1016/J.BCP.2020.113980
REMARK 2
REMARK 2 RESOLUTION. 2.21 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0258
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 20455
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) : 0.196
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.224
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1075
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) : 2.21
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1483
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.49
REMARK 3 BIN R VALUE (WORKING SET) : 0.2900
REMARK 3 BIN FREE R VALUE SET COUNT : 80
REMARK 3 BIN FREE R VALUE : 0.3520
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3281
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 88
REMARK 3 SOLVENT ATOMS : 173
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.41000
REMARK 3 B22 (A**2) : -0.85000
REMARK 3 B33 (A**2) : 3.86000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -2.25000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.330
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3474 ; 0.011 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 3027 ; 0.035 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4701 ; 1.539 ; 1.664
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7056 ; 2.639 ; 1.590
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.928 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;39.079 ;23.944
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;15.314 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.800 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.075 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3876 ; 0.011 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 723 ; 0.035 ; 0.020
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
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 RIDING
REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 6WIA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-20.
REMARK 100 THE DEPOSITION ID IS D_1000246349.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-NOV-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : SEALED TUBE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : APEX
REMARK 200 DATA SCALING SOFTWARE : APEX
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21594
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210
REMARK 200 RESOLUTION RANGE LOW (A) : 41.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.120
REMARK 200 R MERGE (I) : 0.08360
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.5500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 5.05
REMARK 200 R MERGE FOR SHELL (I) : 0.39050
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.360
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 4AZ3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.23
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED IN CRYSTAL SCREEN CRYO II
REMARK 280 CONDITION #12 (0.095 M CADMIUM CHLORIDE HYDRATE, 0.095 M SODIUM
REMARK 280 ACETATE TRIHYDRATE PH 4.6, 28.5% V/V PEG 400, 5% GLYCEROL).
REMARK 280 MOUNTED IN 30% GLYCEROL AND 70% CS CRYO II CONDITION #12.
REMARK 280 PROTEIN WAS INHIBITED WITH DFP IN 25 MM TRIS PH 8, 300 MM NACL
REMARK 280 AT R.T., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.63650
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.99950
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.63650
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.99950
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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 9420 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 32760 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 690 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 HIS A 260
REMARK 465 PHE A 261
REMARK 465 ARG A 262
REMARK 465 TYR A 263
REMARK 465 GLU A 264
REMARK 465 LYS A 265
REMARK 465 ASP A 266
REMARK 465 THR A 267
REMARK 465 VAL A 268
REMARK 465 VAL A 269
REMARK 465 VAL A 270
REMARK 465 GLN A 271
REMARK 465 ASP A 272
REMARK 465 LEU A 273
REMARK 465 GLY A 274
REMARK 465 ASN A 275
REMARK 465 ILE A 276
REMARK 465 PHE A 277
REMARK 465 THR A 278
REMARK 465 ARG A 279
REMARK 465 LEU A 280
REMARK 465 PRO A 281
REMARK 465 LEU A 282
REMARK 465 LYS A 283
REMARK 465 ARG A 284
REMARK 465 MET A 285
REMARK 465 TRP A 286
REMARK 465 HIS A 287
REMARK 465 GLN A 288
REMARK 465 ALA A 289
REMARK 465 LEU A 290
REMARK 465 LEU A 291
REMARK 465 ARG A 292
REMARK 465 SER A 293
REMARK 465 GLY A 294
REMARK 465 ASP A 295
REMARK 465 LYS A 296
REMARK 465 VAL A 297
REMARK 465 ARG A 298
REMARK 465 PRO A 451
REMARK 465 TYR A 452
REMARK 465 HIS A 453
REMARK 465 HIS A 454
REMARK 465 HIS A 455
REMARK 465 HIS A 456
REMARK 465 HIS A 457
REMARK 465 HIS A 458
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 ND2 ASN A 117 C1 NAG A 501 1.69
REMARK 500 O HOH A 642 O HOH A 739 1.88
REMARK 500 O HOH A 750 O HOH A 770 2.17
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 MIS A 150 O - C - N ANGL. DEV. = -10.9 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 GLU A 69 -82.62 -110.61
REMARK 500 VAL A 80 -53.02 -130.08
REMARK 500 PRO A 101 -163.95 -79.67
REMARK 500 MIS A 150 -115.67 66.75
REMARK 500 ASN A 178 59.16 36.51
REMARK 500 ASN A 216 -2.25 76.44
REMARK 500 TYR A 221 -60.93 -94.22
REMARK 500 ASN A 248 98.89 -168.99
REMARK 500 ASP A 404 -71.36 -81.41
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NAG A 501
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 510 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 33 NE2
REMARK 620 2 ASP A 110 OD1 98.6
REMARK 620 3 ASP A 110 OD2 122.8 58.7
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 511 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 166 OD1
REMARK 620 2 ASP A 166 OD2 55.9
REMARK 620 3 SER A 168 OG 62.9 89.2
REMARK 620 4 HOH A 741 O 143.3 93.1 101.6
REMARK 620 5 HOH A 751 O 112.2 165.8 91.5 100.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 513 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 184 OE2
REMARK 620 2 HOH A 648 O 87.7
REMARK 620 3 HOH A 733 O 99.0 80.8
REMARK 620 4 HOH A 729 O 104.5 166.7 92.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 512 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 211 ND1
REMARK 620 2 ASP A 225 OD1 135.6
REMARK 620 3 ASP A 225 OD2 125.6 60.5
REMARK 620 4 ASP A 3 OD1 84.7 65.2 53.4
REMARK 620 5 ASP A 3 OD2 85.0 64.7 53.6 0.7
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 514 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 222 OD1
REMARK 620 2 ASP A 222 OD2 52.9
REMARK 620 3 HOH A 733 O 114.9 89.0
REMARK 620 4 GLU A 326 OE1 67.6 46.8 49.8
REMARK 620 5 HOH A 729 O 107.4 156.7 89.6 118.2
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A 515 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 415 OE1
REMARK 620 2 GLU A 415 OE2 57.5
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 510
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 511
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 512
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 513
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 514
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 515
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 516
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A
REMARK 800 503 through NAG A 504 bound to ASN A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A
REMARK 800 501 through NAG A 502
DBREF 6WIA A 1 452 UNP P10619 PPGB_HUMAN 29 480
SEQADV 6WIA HIS A 453 UNP P10619 EXPRESSION TAG
SEQADV 6WIA HIS A 454 UNP P10619 EXPRESSION TAG
SEQADV 6WIA HIS A 455 UNP P10619 EXPRESSION TAG
SEQADV 6WIA HIS A 456 UNP P10619 EXPRESSION TAG
SEQADV 6WIA HIS A 457 UNP P10619 EXPRESSION TAG
SEQADV 6WIA HIS A 458 UNP P10619 EXPRESSION TAG
SEQRES 1 A 458 ALA PRO ASP GLN ASP GLU ILE GLN ARG LEU PRO GLY LEU
SEQRES 2 A 458 ALA LYS GLN PRO SER PHE ARG GLN TYR SER GLY TYR LEU
SEQRES 3 A 458 LYS GLY SER GLY SER LYS HIS LEU HIS TYR TRP PHE VAL
SEQRES 4 A 458 GLU SER GLN LYS ASP PRO GLU ASN SER PRO VAL VAL LEU
SEQRES 5 A 458 TRP LEU ASN GLY GLY PRO GLY CYS SER SER LEU ASP GLY
SEQRES 6 A 458 LEU LEU THR GLU HIS GLY PRO PHE LEU VAL GLN PRO ASP
SEQRES 7 A 458 GLY VAL THR LEU GLU TYR ASN PRO TYR SER TRP ASN LEU
SEQRES 8 A 458 ILE ALA ASN VAL LEU TYR LEU GLU SER PRO ALA GLY VAL
SEQRES 9 A 458 GLY PHE SER TYR SER ASP ASP LYS PHE TYR ALA THR ASN
SEQRES 10 A 458 ASP THR GLU VAL ALA GLN SER ASN PHE GLU ALA LEU GLN
SEQRES 11 A 458 ASP PHE PHE ARG LEU PHE PRO GLU TYR LYS ASN ASN LYS
SEQRES 12 A 458 LEU PHE LEU THR GLY GLU MIS TYR ALA GLY ILE TYR ILE
SEQRES 13 A 458 PRO THR LEU ALA VAL LEU VAL MET GLN ASP PRO SER MET
SEQRES 14 A 458 ASN LEU GLN GLY LEU ALA VAL GLY ASN GLY LEU SER SER
SEQRES 15 A 458 TYR GLU GLN ASN ASP ASN SER LEU VAL TYR PHE ALA TYR
SEQRES 16 A 458 TYR HIS GLY LEU LEU GLY ASN ARG LEU TRP SER SER LEU
SEQRES 17 A 458 GLN THR HIS CYS CYS SER GLN ASN LYS CYS ASN PHE TYR
SEQRES 18 A 458 ASP ASN LYS ASP LEU GLU CYS VAL THR ASN LEU GLN GLU
SEQRES 19 A 458 VAL ALA ARG ILE VAL GLY ASN SER GLY LEU ASN ILE TYR
SEQRES 20 A 458 ASN LEU TYR ALA PRO CYS ALA GLY GLY VAL PRO SER HIS
SEQRES 21 A 458 PHE ARG TYR GLU LYS ASP THR VAL VAL VAL GLN ASP LEU
SEQRES 22 A 458 GLY ASN ILE PHE THR ARG LEU PRO LEU LYS ARG MET TRP
SEQRES 23 A 458 HIS GLN ALA LEU LEU ARG SER GLY ASP LYS VAL ARG MET
SEQRES 24 A 458 ASP PRO PRO CYS THR ASN THR THR ALA ALA SER THR TYR
SEQRES 25 A 458 LEU ASN ASN PRO TYR VAL ARG LYS ALA LEU ASN ILE PRO
SEQRES 26 A 458 GLU GLN LEU PRO GLN TRP ASP MET CYS ASN PHE LEU VAL
SEQRES 27 A 458 ASN LEU GLN TYR ARG ARG LEU TYR ARG SER MET ASN SER
SEQRES 28 A 458 GLN TYR LEU LYS LEU LEU SER SER GLN LYS TYR GLN ILE
SEQRES 29 A 458 LEU LEU TYR ASN GLY ASP VAL ASP MET ALA CYS ASN PHE
SEQRES 30 A 458 MET GLY ASP GLU TRP PHE VAL ASP SER LEU ASN GLN LYS
SEQRES 31 A 458 MET GLU VAL GLN ARG ARG PRO TRP LEU VAL LYS TYR GLY
SEQRES 32 A 458 ASP SER GLY GLU GLN ILE ALA GLY PHE VAL LYS GLU PHE
SEQRES 33 A 458 SER HIS ILE ALA PHE LEU THR ILE LYS GLY ALA GLY HIS
SEQRES 34 A 458 MET VAL PRO THR ASP LYS PRO LEU ALA ALA PHE THR MET
SEQRES 35 A 458 PHE SER ARG PHE LEU ASN LYS GLN PRO TYR HIS HIS HIS
SEQRES 36 A 458 HIS HIS HIS
MODRES 6WIA MIS A 150 SER MODIFIED RESIDUE
HET MIS A 150 13
HET NAG A 501 14
HET NAG A 502 14
HET NAG A 503 14
HET NAG A 504 14
HET ACT A 505 4
HET ACT A 506 4
HET ACT A 507 4
HET ACT A 508 4
HET ACT A 509 4
HET CD A 510 1
HET CD A 511 1
HET CD A 512 1
HET CD A 513 1
HET CD A 514 1
HET CD A 515 1
HET GOL A 516 6
HETNAM MIS MONOISOPROPYLPHOSPHORYLSERINE
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM ACT ACETATE ION
HETNAM CD CADMIUM ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 MIS C6 H14 N O6 P
FORMUL 2 NAG 4(C8 H15 N O6)
FORMUL 4 ACT 5(C2 H3 O2 1-)
FORMUL 9 CD 6(CD 2+)
FORMUL 15 GOL C3 H8 O3
FORMUL 16 HOH *173(H2 O)
HELIX 1 AA1 SER A 62 GLU A 69 1 8
HELIX 2 AA2 SER A 88 ILE A 92 5 5
HELIX 3 AA3 ASN A 117 PHE A 136 1 20
HELIX 4 AA4 PRO A 137 LYS A 140 5 4
HELIX 5 AA5 TYR A 151 MET A 164 1 14
HELIX 6 AA6 SER A 182 HIS A 197 1 16
HELIX 7 AA7 GLY A 201 CYS A 212 1 12
HELIX 8 AA8 ASP A 225 SER A 242 1 18
HELIX 9 AA9 THR A 306 ASN A 314 1 9
HELIX 10 AB1 ASN A 315 LEU A 322 1 8
HELIX 11 AB2 ASN A 335 TYR A 342 1 8
HELIX 12 AB3 MET A 349 GLN A 360 1 12
HELIX 13 AB4 ASN A 376 LEU A 387 1 12
HELIX 14 AB5 MET A 430 LYS A 435 1 6
HELIX 15 AB6 LYS A 435 ASN A 448 1 14
SHEET 1 AA1 3 GLN A 21 LYS A 27 0
SHEET 2 AA1 3 LYS A 32 VAL A 39 -1 O LEU A 34 N LEU A 26
SHEET 3 AA1 3 TYR A 108 SER A 109 -1 O TYR A 108 N HIS A 33
SHEET 1 AA210 GLN A 21 LYS A 27 0
SHEET 2 AA210 LYS A 32 VAL A 39 -1 O LEU A 34 N LEU A 26
SHEET 3 AA210 ASN A 94 LEU A 98 -1 O TYR A 97 N TRP A 37
SHEET 4 AA210 VAL A 50 LEU A 54 1 N VAL A 51 O ASN A 94
SHEET 5 AA210 LEU A 144 GLU A 149 1 O PHE A 145 N LEU A 52
SHEET 6 AA210 LEU A 171 GLY A 177 1 O GLY A 177 N GLY A 148
SHEET 7 AA210 GLN A 363 GLY A 369 1 O GLN A 363 N GLN A 172
SHEET 8 AA210 ILE A 419 ILE A 424 1 O LEU A 422 N ASN A 368
SHEET 9 AA210 GLY A 406 PHE A 416 -1 N PHE A 412 O THR A 423
SHEET 10 AA210 VAL A 393 TYR A 402 -1 N VAL A 393 O GLU A 415
SHEET 1 AA3 2 PHE A 73 VAL A 75 0
SHEET 2 AA3 2 LEU A 82 TYR A 84 -1 O GLU A 83 N LEU A 74
SHEET 1 AA4 2 CYS A 213 SER A 214 0
SHEET 2 AA4 2 LYS A 217 CYS A 218 -1 O LYS A 217 N SER A 214
SSBOND 1 CYS A 60 CYS A 334 1555 1555 2.11
SSBOND 2 CYS A 212 CYS A 228 1555 1555 2.01
SSBOND 3 CYS A 213 CYS A 218 1555 1555 2.05
SSBOND 4 CYS A 253 CYS A 303 1555 1555 2.05
LINK NE2 HIS A 33 CD CD A 510 1555 1555 2.33
LINK OD1 ASP A 110 CD CD A 510 1555 1555 2.28
LINK OD2 ASP A 110 CD CD A 510 1555 1555 2.19
LINK C GLU A 149 N MIS A 150 1555 1555 1.27
LINK C MIS A 150 N TYR A 151 1555 1555 1.31
LINK OD1 ASP A 166 CD CD A 511 1555 1555 2.36
LINK OD2 ASP A 166 CD CD A 511 1555 1555 2.27
LINK OG SER A 168 CD CD A 511 1555 1555 2.35
LINK OE2 GLU A 184 CD CD A 513 1555 1555 2.26
LINK ND1 HIS A 211 CD CD A 512 1555 1555 2.31
LINK OD1 ASP A 222 CD CD A 514 1555 1555 2.31
LINK OD2 ASP A 222 CD CD A 514 1555 1555 2.37
LINK OD1 ASP A 225 CD CD A 512 1555 1555 2.22
LINK OD2 ASP A 225 CD CD A 512 1555 1555 2.22
LINK ND2 ASN A 305 C1 NAG A 503 1555 1555 1.43
LINK OE1 GLU A 415 CD CD A 515 1555 1555 2.34
LINK OE2 GLU A 415 CD CD A 515 1555 1555 2.22
LINK O4 NAG A 501 C1 NAG A 502 1555 1555 1.44
LINK O4 NAG A 503 C1 NAG A 504 1555 1555 1.36
LINK CD CD A 511 O HOH A 741 1555 1555 2.31
LINK CD CD A 511 O HOH A 751 1555 1555 2.56
LINK CD CD A 513 O HOH A 648 1555 1555 1.97
LINK CD CD A 513 O HOH A 733 1555 1555 2.05
LINK CD CD A 514 O HOH A 733 1555 1555 2.22
LINK OD1 ASP A 3 CD CD A 512 1555 3545 2.67
LINK OD2 ASP A 3 CD CD A 512 1555 3545 2.38
LINK OE1 GLU A 326 CD CD A 514 1555 4546 2.50
LINK CD CD A 513 O HOH A 729 1555 4556 2.59
LINK CD CD A 514 O HOH A 729 1555 4556 2.54
CISPEP 1 GLY A 57 PRO A 58 0 -3.89
CISPEP 2 SER A 100 PRO A 101 0 -2.63
SITE 1 AC1 6 ASN A 55 GLY A 56 GLY A 57 GLU A 149
SITE 2 AC1 6 MIS A 150 HIS A 429
SITE 1 AC2 3 TYR A 183 ASN A 186 ASP A 187
SITE 1 AC3 3 LEU A 354 SER A 358 GLN A 389
SITE 1 AC4 3 GLN A 363 MET A 391 HIS A 418
SITE 1 AC5 4 ASN A 248 HIS A 429 MET A 430 ASP A 434
SITE 1 AC6 2 HIS A 33 ASP A 110
SITE 1 AC7 4 ASP A 166 SER A 168 HOH A 741 HOH A 751
SITE 1 AC8 3 ASP A 3 HIS A 211 ASP A 225
SITE 1 AC9 6 GLU A 184 GLU A 326 CD A 514 HOH A 648
SITE 2 AC9 6 HOH A 729 HOH A 733
SITE 1 AD1 6 ASP A 222 LYS A 320 GLU A 326 CD A 513
SITE 2 AD1 6 HOH A 729 HOH A 733
SITE 1 AD2 1 GLU A 415
SITE 1 AD3 9 TYR A 250 ALA A 251 PRO A 252 TYR A 402
SITE 2 AD3 9 ILE A 409 LYS A 435 HOH A 624 HOH A 649
SITE 3 AD3 9 HOH A 654
SITE 1 AD4 5 PRO A 77 ASP A 78 GLY A 255 ASN A 305
SITE 2 AD4 5 THR A 307
SITE 1 AD5 1 ASN A 117
CRYST1 91.273 101.999 48.114 90.00 101.61 90.00 C 1 2 1 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 0.010956 0.000000 0.002250 0.00000
SCALE2 0.000000 0.009804 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021218 0.00000
TER 3287 GLN A 450
MASTER 489 0 17 15 17 0 20 6 3542 1 131 36
END |