HEADER HYDROLASE/HYDROLASE INHIBITOR 09-DEC-05 2C93
TITLE THROMBIN INHIBITORS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBIN, LIGHT CHAIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: FRAGMENT ALPHA THROMBIN, RESIDUES 328-363;
COMPND 5 EC: 3.4.21.5;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN;
COMPND 8 CHAIN: B;
COMPND 9 FRAGMENT: FRAGMENT ALPHA THROMBIN, RESIDUES 364-622;
COMPND 10 EC: 3.4.21.5;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: HIRUDIN VARIANT-2;
COMPND 13 CHAIN: I;
COMPND 14 FRAGMENT: PEPTIDE FRAGMENT OF HIRUGEN, RESIDUES 61-72;
COMPND 15 SYNONYM: HIRUGEN
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 TISSUE: BLOOD PLASMA;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_COMMON: HUMAN;
SOURCE 9 ORGANISM_TAXID: 9606;
SOURCE 10 TISSUE: BLOOD PLASMA;
SOURCE 11 MOL_ID: 3;
SOURCE 12 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS;
SOURCE 13 ORGANISM_COMMON: MEDICINAL LEECH;
SOURCE 14 ORGANISM_TAXID: 6421
KEYWDS PROTEASE, BLOOD COAGULATION, THROMBIN, GAMMA-CARBOXYGLUTAMIC ACID,
KEYWDS 2 GLYCOPROTEIN, KRINGLE, SERINE PROTEASE, HYDROLASE-HYDROLASE
KEYWDS 3 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.HOWARD,C.ABELL,W.BLAKEMORE,R.CARR,G.CHESSARI,M.CONGREVE,S.HOWARD,
AUTHOR 2 H.JHOTI,C.W.MURRAY,L.C.A.SEAVERS,R.L.M.VAN MONTFORT
REVDAT 7 13-DEC-23 2C93 1 REMARK LINK
REVDAT 6 28-JUN-17 2C93 1 REMARK
REVDAT 5 15-APR-15 2C93 1 SOURCE
REVDAT 4 07-AUG-13 2C93 1 REMARK
REVDAT 3 13-JUL-11 2C93 1 VERSN
REVDAT 2 24-FEB-09 2C93 1 VERSN
REVDAT 1 04-JUL-06 2C93 0
JRNL AUTH N.HOWARD,C.ABELL,W.BLAKEMORE,G.CHESSARI,M.CONGREVE,S.HOWARD,
JRNL AUTH 2 H.JHOTI,C.W.MURRAY,L.C.A.SEAVERS,R.L.M.VAN MONTFORT
JRNL TITL APPLICATION OF FRAGMENT SCREENING AND FRAGMENT LINKING TO
JRNL TITL 2 THE DISCOVERY OF NOVEL THROMBIN INHIBITORS
JRNL REF J.MED.CHEM. V. 49 1346 2006
JRNL REFN ISSN 0022-2623
JRNL PMID 16480269
JRNL DOI 10.1021/JM050850V
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019C
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
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) : 29.11
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 3 NUMBER OF REFLECTIONS : 16625
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) : 0.168
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.242
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 895
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) : 1163
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2000
REMARK 3 BIN FREE R VALUE SET COUNT : 53
REMARK 3 BIN FREE R VALUE : 0.3120
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2362
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 36
REMARK 3 SOLVENT ATOMS : 299
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.28
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.08000
REMARK 3 B22 (A**2) : -0.26000
REMARK 3 B33 (A**2) : -0.10000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.75000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.252
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.687
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2456 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1732 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3317 ; 1.345 ; 1.982
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4179 ; 0.874 ; 3.004
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 6.460 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;38.355 ;23.521
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 437 ;13.997 ;15.137
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.842 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.083 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2675 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 503 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 462 ; 0.220 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1852 ; 0.194 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1145 ; 0.180 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1268 ; 0.082 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 70 ; 0.151 ; 0.200
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): 8 ; 0.166 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.266 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.109 ; 0.200
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): 1443 ; 0.103 ; 5.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2326 ; 0.131 ; 6.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1013 ; 0.143 ; 6.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 991 ; 0.162 ; 7.500
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 : BABINET MODEL WITH 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS. ELECTRON DENSITY PEAKS CLOSE TO PHE 204B AND GLY 193B
REMARK 3 MODELLED AS DMSO.
REMARK 4
REMARK 4 2C93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-05.
REMARK 100 THE DEPOSITION ID IS D_1290026765.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.30
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : CONFOCAL MULTILAYER
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK
REMARK 200 DATA SCALING SOFTWARE : D*TREK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17066
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 29.110
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 200 DATA REDUNDANCY : 1.970
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000
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) : 2.28
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7
REMARK 200 DATA REDUNDANCY IN SHELL : 1.64
REMARK 200 R MERGE FOR SHELL (I) : 0.16000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: IN-HOUSE SOFTWARE
REMARK 200 STARTING MODEL: PDB ENTRY 1QJ1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.30
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 35.32850
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.78050
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.32850
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.78050
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 3990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15490 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.8 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I
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 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 CZ ARG B 75 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B2096 LIES ON A SPECIAL POSITION.
REMARK 400
REMARK 400 COMPOUND
REMARK 400 PROTHROMBIN: CONVERTS FIBRINOGEN TO FIBRIN AND ACTIVATES
REMARK 400 FACTORS V, VII, VIII, XIII, AND, IN COMPLEX WITH
REMARK 400 THROMBOMODULIN.
REMARK 400 HIRUDIN: IT IS A POTENT THROMBIN-SPECIFIC PROTEASE INHIBITOR.
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 THR A -7
REMARK 465 PHE A -6
REMARK 465 GLY A -5
REMARK 465 SER A -4
REMARK 465 ASP A 15
REMARK 465 GLY A 16
REMARK 465 ARG A 17
REMARK 465 THR B 146A
REMARK 465 TRP B 146B
REMARK 465 THR B 146C
REMARK 465 ALA B 146D
REMARK 465 ASN B 146E
REMARK 465 VAL B 147
REMARK 465 GLY B 148
REMARK 465 LYS B 149
REMARK 465 GLY I 54
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN I 65 CA C O CB CG CD OE1
REMARK 470 GLN I 65 NE2
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 OE1 GLN B 151 O HOH B 2163 1.94
REMARK 500 O HOH B 2109 O HOH B 2251 2.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH B 2175 O HOH B 2223 4546 2.07
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 PHE A 7 -91.47 -131.37
REMARK 500 ALA B 44 176.27 179.74
REMARK 500 ASN B 60G 77.05 -152.94
REMARK 500 HIS B 71 -56.70 -127.03
REMARK 500 ASN B 78 -0.40 68.95
REMARK 500 ILE B 79 -61.66 -120.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH B2001 DISTANCE = 5.94 ANGSTROMS
REMARK 525 HOH B2003 DISTANCE = 6.20 ANGSTROMS
REMARK 525 HOH B2006 DISTANCE = 6.89 ANGSTROMS
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 NA B1249 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG B 221A O
REMARK 620 2 LYS B 224 O 93.7
REMARK 620 3 HOH B2200 O 161.4 70.1
REMARK 620 4 HOH B2201 O 89.6 98.5 84.0
REMARK 620 5 HOH B2235 O 105.6 160.5 90.5 79.7
REMARK 620 6 HOH B2241 O 99.0 81.0 87.8 171.4 97.9
REMARK 620 N 1 2 3 4 5
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: DSSP
REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS
REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY
REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
REMARK 700 ARE IDENTICAL.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 1248
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1249
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 1250
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C4M B 1251
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN VARIANT-2
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2C8W RELATED DB: PDB
REMARK 900 THROMBIN INHIBITORS
REMARK 900 RELATED ID: 2C8X RELATED DB: PDB
REMARK 900 THROMBIN INHIBITORS
REMARK 900 RELATED ID: 2C8Y RELATED DB: PDB
REMARK 900 THROMBIN INHIBITORS
REMARK 900 RELATED ID: 2C8Z RELATED DB: PDB
REMARK 900 THROMBIN INHIBITORS
REMARK 900 RELATED ID: 2C90 RELATED DB: PDB
REMARK 900 THROMBIN INHIBITORS
DBREF 2C93 A -7 17 UNP P00734 THRB_HUMAN 328 363
DBREF 2C93 B 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 2C93 I 54 65 UNP P09945 ITH3_HIRME 61 72
SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO
SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG
SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG
SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO
SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU
SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU
SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS
SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE
SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS
SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO
SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU
SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN
SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU
SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR
SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY
SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO
SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN
SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP
SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS
SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU
SEQRES 1 I 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN
MODRES 2C93 TYS I 63 TYR O-SULFO-L-TYROSINE
HET TYS I 63 16
HET DMS B1248 4
HET NA B1249 1
HET DMS B1250 4
HET C4M B1251 27
HETNAM TYS O-SULFO-L-TYROSINE
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM NA SODIUM ION
HETNAM C4M N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-4-METHOXY-
HETNAM 2 C4M 2,3,6-TRIMETHYLBENZENESULFONAMIDE
HETSYN C4M INHIBITOR OF THROMBIN
FORMUL 3 TYS C9 H11 N O6 S
FORMUL 4 DMS 2(C2 H6 O S)
FORMUL 5 NA NA 1+
FORMUL 7 C4M C20 H28 N2 O4 S
FORMUL 8 HOH *299(H2 O)
HELIX 1 1 PHE A 7 SER A 11 5 5
HELIX 2 2 THR A 14B TYR A 14J 1 9
HELIX 3 3 ALA B 55 CYS B 58 5 4
HELIX 4 4 PRO B 60B ASP B 60E 5 4
HELIX 5 5 THR B 60I ASN B 62 5 3
HELIX 6 6 ASP B 125 LEU B 130 1 9
HELIX 7 7 GLU B 164 SER B 171 1 8
HELIX 8 8 LEU B 234 GLY B 246 1 13
HELIX 9 9 PRO I 60 LEU I 64 5 5
SHEET 1 BA 7 SER B 20 ASP B 21 0
SHEET 2 BA 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20
SHEET 3 BA 7 LYS B 135 GLY B 140 -1 O GLY B 136 N LEU B 160
SHEET 4 BA 7 PRO B 198 LYS B 202 -1 O PRO B 198 N THR B 139
SHEET 5 BA 7 TRP B 207 TRP B 215 -1 O TYR B 208 N MET B 201
SHEET 6 BA 7 GLY B 226 HIS B 230 -1 O PHE B 227 N SER B 214
SHEET 7 BA 7 MET B 180 ALA B 183 -1 O PHE B 181 N TYR B 228
SHEET 1 BB 7 GLN B 30 ARG B 35 0
SHEET 2 BB 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35
SHEET 3 BB 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45
SHEET 4 BB 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54
SHEET 5 BB 7 LYS B 81 ILE B 90 -1 N GLU B 86 O LYS B 107
SHEET 6 BB 7 LEU B 64 ILE B 68 -1 O LEU B 64 N LEU B 85
SHEET 7 BB 7 GLN B 30 ARG B 35 -1 O MET B 32 N ARG B 67
SHEET 1 BC 2 LEU B 60 TYR B 60A 0
SHEET 2 BC 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A
SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.06
SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.04
SSBOND 3 CYS B 168 CYS B 182 1555 1555 1.98
SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.02
LINK C GLU I 62 N TYS I 63 1555 1555 1.33
LINK C TYS I 63 N LEU I 64 1555 1555 1.33
LINK O ARG B 221A NA NA B1249 1555 1555 2.37
LINK O LYS B 224 NA NA B1249 1555 1555 2.39
LINK NA NA B1249 O HOH B2200 1555 1555 2.54
LINK NA NA B1249 O HOH B2201 1555 1555 2.73
LINK NA NA B1249 O HOH B2235 1555 1555 2.48
LINK NA NA B1249 O HOH B2241 1555 1555 2.28
CISPEP 1 SER B 37 PRO B 37A 0 -5.31
SITE 1 AC1 4 GLU B 127 SER B 129B GLY B 223 LYS B 224
SITE 1 AC2 6 ARG B 221A LYS B 224 HOH B2200 HOH B2201
SITE 2 AC2 6 HOH B2235 HOH B2241
SITE 1 AC3 10 LEU B 41 CYS B 42 HIS B 57 GLU B 192
SITE 2 AC3 10 GLY B 193 ASP B 194 SER B 195 C4M B1251
SITE 3 AC3 10 HOH B2051 HOH B2065
SITE 1 AC4 11 HIS B 57 TYR B 60A TRP B 60D TRP B 96
SITE 2 AC4 11 LEU B 99 GLU B 192 TRP B 215 GLY B 216
SITE 3 AC4 11 DMS B1250 HOH B2231 HOH B2256
SITE 1 AC5 15 PHE B 34 GLN B 38 LEU B 65 ARG B 67
SITE 2 AC5 15 ARG B 73 THR B 74 ARG B 75 TYR B 76
SITE 3 AC5 15 LYS B 81 ILE B 82 SER B 153 HOH B2091
SITE 4 AC5 15 HOH I2001 HOH I2002 HOH I2003
CRYST1 70.657 71.561 71.960 90.00 100.65 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 0.014153 0.000000 0.002661 0.00000
SCALE2 0.000000 0.013974 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014140 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
