| content |
HEADER HYDROLASE/HYDROLASE INHIBITOR 17-OCT-13 3WK7
TITLE CRYSTAL STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE IN COMPLEX WITH
TITLE 2 FRAGMENT INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BIFUNCTIONAL EPOXIDE HYDROLASE 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CYTOSOLIC EPOXIDE HYDROLASE 2, CEH, EPOXIDE HYDRATASE,
COMPND 5 SOLUBLE EPOXIDE HYDROLASE, SEH, LIPID-PHOSPHATE PHOSPHATASE;
COMPND 6 EC: 3.3.2.10, 3.1.3.76;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: EPHX2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.AMANO,T.YAMAGUCHI,E.TANABE
REVDAT 1 16-APR-14 3WK7 0
JRNL AUTH Y.AMANO,T.YAMAGUCHI,E.TANABE
JRNL TITL STRUCTURAL INSIGHTS INTO BINDING OF INHIBITORS TO SOLUBLE
JRNL TITL 2 EPOXIDE HYDROLASE GAINED BY FRAGMENT SCREENING AND X-RAY
JRNL TITL 3 CRYSTALLOGRAPHY
JRNL REF BIOORG.MED.CHEM. 2014
JRNL REFN ESSN 1464-3391
JRNL PMID 24656800
JRNL DOI 10.1016/J.BMC.2014.03.001
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.11
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 30088
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) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.204
REMARK 3 FREE R VALUE : 0.259
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1613
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2188
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.18
REMARK 3 BIN R VALUE (WORKING SET) : 0.2430
REMARK 3 BIN FREE R VALUE SET COUNT : 118
REMARK 3 BIN FREE R VALUE : 0.3720
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4323
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 21
REMARK 3 SOLVENT ATOMS : 70
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.67
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.05000
REMARK 3 B22 (A**2) : 0.05000
REMARK 3 B33 (A**2) : -0.16000
REMARK 3 B12 (A**2) : 0.05000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.274
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.224
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.316
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4449 ; 0.017 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6030 ; 2.019 ; 1.976
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 545 ; 7.191 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;34.921 ;24.167
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 783 ;18.764 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.695 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 659 ; 0.128 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3372 ; 0.010 ; 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): 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 : MASK
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: NULL
REMARK 4
REMARK 4 3WK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-13.
REMARK 100 THE RCSB ID CODE IS RCSB096438.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 90
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NE3A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30088
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 30.110
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.47
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M POTASSIUM PHOSPHATE, 0.2M
REMARK 280 AMMONIUM DIHYDROGEN PHOSPHATE, 25%W/V PEG 3350, PH 7.5, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 162.97267
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.48633
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 122.22950
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.74317
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 203.71583
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 162.97267
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 81.48633
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.74317
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 122.22950
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 203.71583
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: 4850 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 42840 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 -92.69700
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 122.22950
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 MET A 1
REMARK 465 ASN A 548
REMARK 465 PRO A 549
REMARK 465 PRO A 550
REMARK 465 VAL A 551
REMARK 465 VAL A 552
REMARK 465 SER A 553
REMARK 465 LYS A 554
REMARK 465 MET A 555
REMARK 465 HIS A 556
REMARK 465 HIS A 557
REMARK 465 HIS A 558
REMARK 465 HIS A 559
REMARK 465 HIS A 560
REMARK 465 HIS A 561
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 ARG A 130 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES
REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES
REMARK 500 ARG A 287 CD - NE - CZ ANGL. DEV. = 8.4 DEGREES
REMARK 500 ARG A 287 NE - CZ - NH1 ANGL. DEV. = -6.7 DEGREES
REMARK 500 ARG A 287 NE - CZ - NH2 ANGL. DEV. = 8.8 DEGREES
REMARK 500 ARG A 471 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES
REMARK 500 ARG A 471 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ARG A 482 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES
REMARK 500 ARG A 482 NE - CZ - NH2 ANGL. DEV. = 4.7 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 LEU A 10 -70.18 -96.68
REMARK 500 VAL A 13 -65.07 -127.72
REMARK 500 ALA A 131 -38.53 -36.87
REMARK 500 GLN A 204 -105.11 -96.92
REMARK 500 GLU A 269 -134.53 -125.84
REMARK 500 SER A 270 161.20 178.39
REMARK 500 ASP A 335 -132.49 65.34
REMARK 500 ASN A 359 -46.42 73.64
REMARK 500 ALA A 377 44.62 -86.44
REMARK 500 ASN A 378 97.37 -174.34
REMARK 500 MET A 419 31.97 -91.81
REMARK 500 LYS A 421 59.03 37.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 MET A 291 ASP A 292 138.62
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 VAL A 19 23.4 L L OUTSIDE RANGE
REMARK 500 ARG A 247 24.1 L L OUTSIDE RANGE
REMARK 500 TYR A 343 24.7 L L OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
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 MG A 601 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 9 OD2
REMARK 620 2 PO4 A 602 O1 88.9
REMARK 620 3 ASP A 11 O 76.8 101.2
REMARK 620 4 ASP A 185 OD1 79.3 163.6 87.2
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE S0D A 603
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3WK4 RELATED DB: PDB
REMARK 900 RELATED ID: 3WK5 RELATED DB: PDB
REMARK 900 RELATED ID: 3WK6 RELATED DB: PDB
REMARK 900 RELATED ID: 3WK8 RELATED DB: PDB
REMARK 900 RELATED ID: 3WK9 RELATED DB: PDB
REMARK 900 RELATED ID: 3WKA RELATED DB: PDB
REMARK 900 RELATED ID: 3WKB RELATED DB: PDB
REMARK 900 RELATED ID: 3WKC RELATED DB: PDB
REMARK 900 RELATED ID: 3WKD RELATED DB: PDB
REMARK 900 RELATED ID: 3WKE RELATED DB: PDB
DBREF 3WK7 A 1 555 UNP P34913 HYES_HUMAN 1 555
SEQADV 3WK7 HIS A 556 UNP P34913 EXPRESSION TAG
SEQADV 3WK7 HIS A 557 UNP P34913 EXPRESSION TAG
SEQADV 3WK7 HIS A 558 UNP P34913 EXPRESSION TAG
SEQADV 3WK7 HIS A 559 UNP P34913 EXPRESSION TAG
SEQADV 3WK7 HIS A 560 UNP P34913 EXPRESSION TAG
SEQADV 3WK7 HIS A 561 UNP P34913 EXPRESSION TAG
SEQRES 1 A 561 MET THR LEU ARG ALA ALA VAL PHE ASP LEU ASP GLY VAL
SEQRES 2 A 561 LEU ALA LEU PRO ALA VAL PHE GLY VAL LEU GLY ARG THR
SEQRES 3 A 561 GLU GLU ALA LEU ALA LEU PRO ARG GLY LEU LEU ASN ASP
SEQRES 4 A 561 ALA PHE GLN LYS GLY GLY PRO GLU GLY ALA THR THR ARG
SEQRES 5 A 561 LEU MET LYS GLY GLU ILE THR LEU SER GLN TRP ILE PRO
SEQRES 6 A 561 LEU MET GLU GLU ASN CYS ARG LYS CYS SER GLU THR ALA
SEQRES 7 A 561 LYS VAL CYS LEU PRO LYS ASN PHE SER ILE LYS GLU ILE
SEQRES 8 A 561 PHE ASP LYS ALA ILE SER ALA ARG LYS ILE ASN ARG PRO
SEQRES 9 A 561 MET LEU GLN ALA ALA LEU MET LEU ARG LYS LYS GLY PHE
SEQRES 10 A 561 THR THR ALA ILE LEU THR ASN THR TRP LEU ASP ASP ARG
SEQRES 11 A 561 ALA GLU ARG ASP GLY LEU ALA GLN LEU MET CYS GLU LEU
SEQRES 12 A 561 LYS MET HIS PHE ASP PHE LEU ILE GLU SER CYS GLN VAL
SEQRES 13 A 561 GLY MET VAL LYS PRO GLU PRO GLN ILE TYR LYS PHE LEU
SEQRES 14 A 561 LEU ASP THR LEU LYS ALA SER PRO SER GLU VAL VAL PHE
SEQRES 15 A 561 LEU ASP ASP ILE GLY ALA ASN LEU LYS PRO ALA ARG ASP
SEQRES 16 A 561 LEU GLY MET VAL THR ILE LEU VAL GLN ASP THR ASP THR
SEQRES 17 A 561 ALA LEU LYS GLU LEU GLU LYS VAL THR GLY ILE GLN LEU
SEQRES 18 A 561 LEU ASN THR PRO ALA PRO LEU PRO THR SER CYS ASN PRO
SEQRES 19 A 561 SER ASP MET SER HIS GLY TYR VAL THR VAL LYS PRO ARG
SEQRES 20 A 561 VAL ARG LEU HIS PHE VAL GLU LEU GLY SER GLY PRO ALA
SEQRES 21 A 561 VAL CYS LEU CYS HIS GLY PHE PRO GLU SER TRP TYR SER
SEQRES 22 A 561 TRP ARG TYR GLN ILE PRO ALA LEU ALA GLN ALA GLY TYR
SEQRES 23 A 561 ARG VAL LEU ALA MET ASP MET LYS GLY TYR GLY GLU SER
SEQRES 24 A 561 SER ALA PRO PRO GLU ILE GLU GLU TYR CYS MET GLU VAL
SEQRES 25 A 561 LEU CYS LYS GLU MET VAL THR PHE LEU ASP LYS LEU GLY
SEQRES 26 A 561 LEU SER GLN ALA VAL PHE ILE GLY HIS ASP TRP GLY GLY
SEQRES 27 A 561 MET LEU VAL TRP TYR MET ALA LEU PHE TYR PRO GLU ARG
SEQRES 28 A 561 VAL ARG ALA VAL ALA SER LEU ASN THR PRO PHE ILE PRO
SEQRES 29 A 561 ALA ASN PRO ASN MET SER PRO LEU GLU SER ILE LYS ALA
SEQRES 30 A 561 ASN PRO VAL PHE ASP TYR GLN LEU TYR PHE GLN GLU PRO
SEQRES 31 A 561 GLY VAL ALA GLU ALA GLU LEU GLU GLN ASN LEU SER ARG
SEQRES 32 A 561 THR PHE LYS SER LEU PHE ARG ALA SER ASP GLU SER VAL
SEQRES 33 A 561 LEU SER MET HIS LYS VAL CYS GLU ALA GLY GLY LEU PHE
SEQRES 34 A 561 VAL ASN SER PRO GLU GLU PRO SER LEU SER ARG MET VAL
SEQRES 35 A 561 THR GLU GLU GLU ILE GLN PHE TYR VAL GLN GLN PHE LYS
SEQRES 36 A 561 LYS SER GLY PHE ARG GLY PRO LEU ASN TRP TYR ARG ASN
SEQRES 37 A 561 MET GLU ARG ASN TRP LYS TRP ALA CYS LYS SER LEU GLY
SEQRES 38 A 561 ARG LYS ILE LEU ILE PRO ALA LEU MET VAL THR ALA GLU
SEQRES 39 A 561 LYS ASP PHE VAL LEU VAL PRO GLN MET SER GLN HIS MET
SEQRES 40 A 561 GLU ASP TRP ILE PRO HIS LEU LYS ARG GLY HIS ILE GLU
SEQRES 41 A 561 ASP CYS GLY HIS TRP THR GLN MET ASP LYS PRO THR GLU
SEQRES 42 A 561 VAL ASN GLN ILE LEU ILE LYS TRP LEU ASP SER ASP ALA
SEQRES 43 A 561 ARG ASN PRO PRO VAL VAL SER LYS MET HIS HIS HIS HIS
SEQRES 44 A 561 HIS HIS
HET MG A 601 1
HET PO4 A 602 5
HET S0D A 603 15
HETNAM MG MAGNESIUM ION
HETNAM PO4 PHOSPHATE ION
HETNAM S0D 2-(1-METHYL-1H-PYRAZOL-4-YL)-1H-BENZIMIDAZOLE
FORMUL 2 MG MG 2+
FORMUL 3 PO4 O4 P 3-
FORMUL 4 S0D C11 H10 N4
FORMUL 5 HOH *70(H2 O)
HELIX 1 1 ALA A 18 LEU A 30 1 13
HELIX 2 2 GLY A 35 LYS A 43 1 9
HELIX 3 3 GLY A 44 GLU A 47 5 4
HELIX 4 4 GLY A 48 LYS A 55 1 8
HELIX 5 5 THR A 59 ALA A 78 1 20
HELIX 6 6 SER A 87 ARG A 99 1 13
HELIX 7 7 ASN A 102 LYS A 115 1 14
HELIX 8 8 ARG A 133 MET A 145 1 13
HELIX 9 9 SER A 153 GLY A 157 1 5
HELIX 10 10 GLU A 162 LYS A 174 1 13
HELIX 11 11 SER A 176 SER A 178 5 3
HELIX 12 12 ILE A 186 LEU A 196 1 11
HELIX 13 13 ASP A 205 GLY A 218 1 14
HELIX 14 14 ASN A 233 MET A 237 5 5
HELIX 15 15 SER A 270 ARG A 275 5 6
HELIX 16 16 TYR A 276 ALA A 284 1 9
HELIX 17 17 GLU A 304 TYR A 308 5 5
HELIX 18 18 CYS A 309 GLY A 325 1 17
HELIX 19 19 ASP A 335 TYR A 348 1 14
HELIX 20 20 SER A 370 ALA A 377 1 8
HELIX 21 21 ASN A 378 VAL A 380 5 3
HELIX 22 22 PHE A 381 GLN A 388 1 8
HELIX 23 23 GLY A 391 ASN A 400 1 10
HELIX 24 24 ASN A 400 PHE A 409 1 10
HELIX 25 25 LYS A 421 GLY A 426 1 6
HELIX 26 26 THR A 443 GLY A 458 1 16
HELIX 27 27 PHE A 459 TRP A 465 1 7
HELIX 28 28 ASN A 468 LYS A 478 1 11
HELIX 29 29 VAL A 500 GLN A 505 5 6
HELIX 30 30 HIS A 506 TRP A 510 5 5
HELIX 31 31 TRP A 525 LYS A 530 1 6
HELIX 32 32 LYS A 530 ALA A 546 1 17
SHEET 1 A 5 PHE A 149 GLU A 152 0
SHEET 2 A 5 THR A 118 THR A 123 1 N ILE A 121 O ILE A 151
SHEET 3 A 5 ALA A 5 PHE A 8 1 N PHE A 8 O ALA A 120
SHEET 4 A 5 VAL A 180 ASP A 184 1 O LEU A 183 N VAL A 7
SHEET 5 A 5 VAL A 199 LEU A 202 1 O ILE A 201 N ASP A 184
SHEET 1 B 2 ALA A 15 LEU A 16 0
SHEET 2 B 2 LYS A 100 ILE A 101 -1 O LYS A 100 N LEU A 16
SHEET 1 C 8 SER A 238 LYS A 245 0
SHEET 2 C 8 VAL A 248 LEU A 255 -1 O PHE A 252 N GLY A 240
SHEET 3 C 8 ARG A 287 ASP A 292 -1 O VAL A 288 N LEU A 255
SHEET 4 C 8 ALA A 260 CYS A 264 1 N VAL A 261 O LEU A 289
SHEET 5 C 8 ALA A 329 HIS A 334 1 O VAL A 330 N ALA A 260
SHEET 6 C 8 VAL A 352 LEU A 358 1 O ALA A 356 N PHE A 331
SHEET 7 C 8 ALA A 488 ALA A 493 1 O VAL A 491 N SER A 357
SHEET 8 C 8 LYS A 515 ILE A 519 1 O LYS A 515 N MET A 490
LINK OD2 ASP A 9 MG MG A 601 1555 1555 2.08
LINK MG MG A 601 O1 PO4 A 602 1555 1555 2.10
LINK O ASP A 11 MG MG A 601 1555 1555 2.19
LINK OD1 ASP A 185 MG MG A 601 1555 1555 2.19
CISPEP 1 LEU A 16 PRO A 17 0 -20.13
CISPEP 2 LYS A 160 PRO A 161 0 3.20
CISPEP 3 PHE A 267 PRO A 268 0 -8.88
SITE 1 AC1 4 ASP A 9 ASP A 11 ASP A 185 PO4 A 602
SITE 1 AC2 6 ASP A 9 ASP A 11 THR A 123 ASN A 124
SITE 2 AC2 6 LYS A 160 MG A 601
SITE 1 AC3 6 PHE A 267 ASP A 335 TRP A 336 TYR A 383
SITE 2 AC3 6 GLN A 384 TYR A 466
CRYST1 92.697 92.697 244.459 90.00 90.00 120.00 P 65 2 2 12
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 0.010788 0.006228 0.000000 0.00000
SCALE2 0.000000 0.012457 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004091 0.00000
TER 4324 ARG A 547
MASTER 421 0 3 32 15 0 5 6 4414 1 24 44
END |