HEADER HYDROLASE/HYDROLASE INHIBITOR 18-JUN-07 2V3H
TITLE THROMBIN WITH 3-CYCLE NO F
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN;
COMPND 3 CHAIN: H;
COMPND 4 FRAGMENT: CATALYTIC, RESIDUES 364-620;
COMPND 5 EC: 3.4.21.5;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: HIRUDIN IIA;
COMPND 9 CHAIN: I;
COMPND 10 FRAGMENT: C-TERMINUS, RESIDUES 56-65;
COMPND 11 ENGINEERED: YES;
COMPND 12 OTHER_DETAILS: THE N-TERMINAL ASP IS DES-AMINO - I.E. SUCCINIC ACID;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: THROMBIN LIGHT CHAIN;
COMPND 15 CHAIN: L;
COMPND 16 FRAGMENT: LIGHT CHAIN, RESIDUES 334-361;
COMPND 17 EC: 3.4.21.5;
COMPND 18 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029;
SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: OVARY;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS;
SOURCE 12 ORGANISM_COMMON: MEDICINAL LEECH;
SOURCE 13 ORGANISM_TAXID: 6421;
SOURCE 14 MOL_ID: 3;
SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 16 ORGANISM_COMMON: HUMAN;
SOURCE 17 ORGANISM_TAXID: 9606;
SOURCE 18 EXPRESSION_SYSTEM: CRICETULUS GRISEUS;
SOURCE 19 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER;
SOURCE 20 EXPRESSION_SYSTEM_TAXID: 10029;
SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: OVARY
KEYWDS SERINE PROTEASE INHIBITOR COMPLEX, BLOOD CLOTTING, GAMMA-
KEYWDS 2 CARBOXYGLUTAMIC ACID, SERINE PROTEASE, CALCIUM-BINDING, DISEASE
KEYWDS 3 MUTATION, BLOOD COAGULATION, SULFATION, ACUTE PHASE, GLYCOPROTEIN,
KEYWDS 4 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR D.W.BANNER,U.OBST
REVDAT 5 07-AUG-13 2V3H 1 REMARK
REVDAT 4 13-JUL-11 2V3H 1 VERSN
REVDAT 3 24-FEB-09 2V3H 1 VERSN
REVDAT 2 01-JUL-08 2V3H 1 SOURCE
REVDAT 1 24-JUN-08 2V3H 0
JRNL AUTH K.MUELLER,C.FAEH,F.DIEDERICH
JRNL TITL FLUORINE IN PHARMACEUTICALS: LOOKING BEYOND INTUITION.
JRNL REF SCIENCE V. 317 1881 2007
JRNL REFN ISSN 0036-8075
JRNL PMID 17901324
JRNL DOI 10.1126/SCIENCE.1131943
REMARK 2
REMARK 2 RESOLUTION. 1.79 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 1.79
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.25
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1
REMARK 3 NUMBER OF REFLECTIONS : 29198
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) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.207
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1556
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) : 1.79
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1947
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2290
REMARK 3 BIN FREE R VALUE SET COUNT : 97
REMARK 3 BIN FREE R VALUE : 0.2210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2307
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 392
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 27.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.81
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.40000
REMARK 3 B22 (A**2) : -1.26000
REMARK 3 B33 (A**2) : 0.38000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.32000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.126
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.228
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2424 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3270 ; 1.340 ; 1.978
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.080 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;30.394 ;23.130
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;11.868 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;11.621 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.093 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1847 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1083 ; 0.196 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1606 ; 0.310 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 312 ; 0.152 ; 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): 24 ; 0.159 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.199 ; 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): 1422 ; 0.625 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 1.058 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1060 ; 1.771 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 977 ; 2.507 ; 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 : 3
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 : L 1 L 14
REMARK 3 ORIGIN FOR THE GROUP (A): -0.0190 10.7600 24.4330
REMARK 3 T TENSOR
REMARK 3 T11: -0.1255 T22: -0.1741
REMARK 3 T33: -0.1446 T12: 0.0366
REMARK 3 T13: 0.0245 T23: -0.0169
REMARK 3 L TENSOR
REMARK 3 L11: 2.1536 L22: 2.2051
REMARK 3 L33: 2.8037 L12: -0.3417
REMARK 3 L13: -0.2369 L23: -0.9555
REMARK 3 S TENSOR
REMARK 3 S11: 0.0478 S12: -0.0362 S13: 0.0685
REMARK 3 S21: 0.0743 S22: -0.0382 S23: 0.0534
REMARK 3 S31: -0.1727 S32: -0.1648 S33: -0.0096
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 : H 16 H 245
REMARK 3 ORIGIN FOR THE GROUP (A): 14.2140 -0.9040 19.7180
REMARK 3 T TENSOR
REMARK 3 T11: -0.1281 T22: -0.1736
REMARK 3 T33: -0.1405 T12: 0.0193
REMARK 3 T13: 0.0226 T23: -0.0101
REMARK 3 L TENSOR
REMARK 3 L11: 1.5903 L22: 1.1911
REMARK 3 L33: 1.2537 L12: -0.7605
REMARK 3 L13: 0.0498 L23: -0.1314
REMARK 3 S TENSOR
REMARK 3 S11: 0.0775 S12: 0.0870 S13: -0.0487
REMARK 3 S21: -0.0782 S22: -0.0838 S23: -0.0338
REMARK 3 S31: 0.0827 S32: 0.0905 S33: 0.0063
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 : I 2 I 6
REMARK 3 ORIGIN FOR THE GROUP (A): 8.7720 -3.6820 -2.4200
REMARK 3 T TENSOR
REMARK 3 T11: 0.1195 T22: 0.1501
REMARK 3 T33: -0.0118 T12: 0.1656
REMARK 3 T13: -0.0105 T23: -0.0536
REMARK 3 L TENSOR
REMARK 3 L11: 3.6326 L22: 5.5917
REMARK 3 L33: 15.5361 L12: 4.4784
REMARK 3 L13: -4.7831 L23: -5.0893
REMARK 3 S TENSOR
REMARK 3 S11: 0.4861 S12: 0.2002 S13: -0.0217
REMARK 3 S21: -0.6747 S22: -0.8171 S23: -0.6947
REMARK 3 S31: 0.1839 S32: 1.0017 S33: 0.3310
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 2V3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-07.
REMARK 100 THE PDBE ID CODE IS EBI-32908.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-NOV-99
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
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 : ENRAF-NONIUS FR571
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC MAXFLUX
REMARK 200 OPTICS : OSMIC MAXFLUX
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30755
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4
REMARK 200 DATA REDUNDANCY : 2.740
REMARK 200 R MERGE (I) : 0.04000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 48.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.71
REMARK 200 R MERGE FOR SHELL (I) : 0.21000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: CCP4
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 35.22000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.89000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.22000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.89000
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: TRIMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 3540 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15720 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.5 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, I, L
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 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 TRP H 147A
REMARK 465 THR H 147B
REMARK 465 ALA H 147C
REMARK 465 ASN H 147D
REMARK 465 VAL H 147E
REMARK 465 GLY H 147F
REMARK 465 LYS H 147G
REMARK 465 GLU I 7
REMARK 465 GLU I 8
REMARK 465 TYR I 9
REMARK 465 LEU I 10
REMARK 465 GLN I 11
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 HOH H 2106 O HOH H 2245 1.82
REMARK 500 O HOH H 2096 O HOH H 2098 2.09
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 CYS H 182 CA - CB - SG ANGL. DEV. = 7.3 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 CYS H 42 169.78 179.15
REMARK 500 TYR H 60A 81.83 -153.25
REMARK 500 ASN H 60G 81.83 -154.74
REMARK 500 HIS H 71 -61.90 -124.61
REMARK 500 ILE H 79 -62.30 -129.45
REMARK 500 GLU H 97A -72.75 -118.65
REMARK 500 SER H 214 -77.42 -107.92
REMARK 500 PHE L 7 -94.02 -129.01
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 NA H1247 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG H 221A O
REMARK 620 2 HOH H2306 O 103.0
REMARK 620 3 LYS H 224 O 99.0 84.9
REMARK 620 4 HOH H2260 O 161.4 89.9 68.5
REMARK 620 5 HOH H2298 O 106.1 94.8 154.3 85.8
REMARK 620 6 HOH H2261 O 88.4 167.5 98.4 80.3 76.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA H1248 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH H2238 O
REMARK 620 2 LYS H 169 O 59.2
REMARK 620 3 HOH H2103 O 71.3 117.3
REMARK 620 4 HOH H2239 O 99.7 78.1 74.8
REMARK 620 5 THR H 172 O 74.8 74.3 127.7 150.5
REMARK 620 6 HOH H2281 O 120.7 163.9 75.0 116.5 90.0
REMARK 620 7 PHE H 204A O 151.7 93.3 133.7 79.2 92.1 83.6
REMARK 620 N 1 2 3 4 5 6
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: DSSP
REMARK 700 THE SHEETS PRESENTED AS "HB" 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 I25 H 1246
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1247
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 1248
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIA
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2V3O RELATED DB: PDB
REMARK 900 THROMBIN WITH 3-CYCLE WITH F
DBREF 2V3H H 16 245 UNP P00734 THRB_HUMAN 364 620
DBREF 2V3H I 1 1 PDB 2V3H 2V3H 1 1
DBREF 2V3H I 2 11 UNP P28503 ITHC_HIRME 56 65
DBREF 2V3H L 1B 14L UNP P00734 THRB_HUMAN 334 361
SEQRES 1 H 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO
SEQRES 2 H 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU
SEQRES 3 H 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU
SEQRES 4 H 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS
SEQRES 5 H 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 H 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE
SEQRES 7 H 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 H 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS
SEQRES 9 H 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO
SEQRES 10 H 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU
SEQRES 11 H 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 H 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN
SEQRES 13 H 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU
SEQRES 14 H 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR
SEQRES 15 H 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY
SEQRES 16 H 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO
SEQRES 17 H 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN
SEQRES 18 H 257 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP
SEQRES 19 H 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS
SEQRES 20 H 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE
SEQRES 1 I 11 SIN PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN
SEQRES 1 L 28 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER
SEQRES 2 L 28 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR
SEQRES 3 L 28 ILE ASP
HET SIN I 1 7
HET I25 H1246 31
HET NA H1247 1
HET CA H1248 1
HETNAM SIN SUCCINIC ACID
HETNAM I25 (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-
HETNAM 2 I25 (DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-
HETNAM 3 I25 ETHYLPHENYL}ACETIC ACID
HETNAM NA SODIUM ION
HETNAM CA CALCIUM ION
FORMUL 2 SIN C4 H6 O4
FORMUL 4 I25 C24 H34 N4 O3
FORMUL 5 NA NA 1+
FORMUL 6 CA CA 2+
FORMUL 7 HOH *392(H2 O)
HELIX 1 1 ALA H 55 CYS H 58 5 4
HELIX 2 2 PRO H 60B ASP H 60E 5 4
HELIX 3 3 THR H 60I ASN H 62 5 3
HELIX 4 4 ASP H 125 LEU H 130 1 9
HELIX 5 5 GLU H 164 SER H 171 1 8
HELIX 6 6 LYS H 185 GLY H 186C 5 5
HELIX 7 7 LEU H 234 PHE H 245 1 12
HELIX 8 8 PHE L 7 SER L 11 5 5
HELIX 9 9 THR L 14B TYR L 14J 1 9
SHEET 1 HA 7 SER H 20 ASP H 21 0
SHEET 2 HA 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20
SHEET 3 HA 7 LYS H 135 GLY H 140 -1 O GLY H 136 N LEU H 160
SHEET 4 HA 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139
SHEET 5 HA 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201
SHEET 6 HA 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214
SHEET 7 HA 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228
SHEET 1 HB 7 GLN H 30 ARG H 35 0
SHEET 2 HB 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35
SHEET 3 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45
SHEET 4 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54
SHEET 5 HB 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107
SHEET 6 HB 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85
SHEET 7 HB 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67
SHEET 1 HC 2 LEU H 60 TYR H 60A 0
SHEET 2 HC 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A
SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.03
SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.02
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05
LINK NA NA H1247 O ARG H 221A 1555 1555 2.26
LINK NA NA H1247 O HOH H2306 1555 1555 2.25
LINK NA NA H1247 O LYS H 224 1555 1555 2.27
LINK CA CA H1248 O HOH H2238 1555 1555 2.97
LINK CA CA H1248 O LYS H 169 1555 1555 2.59
LINK CA CA H1248 O HOH H2103 1555 1555 3.12
LINK CA CA H1248 O HOH H2239 1555 1555 2.81
LINK CA CA H1248 O THR H 172 1555 1555 2.61
LINK CA CA H1248 O HOH H2281 1555 4546 2.61
LINK CA CA H1248 O PHE H 204A 1555 4546 2.57
LINK C4 SIN I 1 N PHE I 2 1555 1555 1.26
LINK NA NA H1247 O HOH H2260 1555 1555 2.64
LINK NA NA H1247 O HOH H2298 1555 1555 2.66
LINK NA NA H1247 O HOH H2261 1555 1555 2.74
CISPEP 1 SER H 36A PRO H 37 0 -10.63
SITE 1 AC1 16 HIS H 57 TYR H 60A LEU H 99 ASP H 189
SITE 2 AC1 16 ALA H 190 GLU H 192 SER H 195 SER H 214
SITE 3 AC1 16 TRP H 215 GLY H 216 GLY H 219 GLY H 226
SITE 4 AC1 16 HOH H2275 HOH H2296 HOH H2325 HOH H2326
SITE 1 AC2 6 ARG H 221A LYS H 224 HOH H2260 HOH H2261
SITE 2 AC2 6 HOH H2298 HOH H2306
SITE 1 AC3 6 LYS H 169 THR H 172 PHE H 204A HOH H2238
SITE 2 AC3 6 HOH H2239 HOH H2281
SITE 1 AC4 13 PHE H 34 GLN H 38 ARG H 67 ARG H 73
SITE 2 AC4 13 THR H 74 ARG H 75 TYR H 76 ILE H 82
SITE 3 AC4 13 HOH H2117 HOH H2121 HOH H2122 HOH H2124
SITE 4 AC4 13 HOH I2001
CRYST1 70.440 71.780 72.410 90.00 100.40 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 0.014196 0.000000 0.002606 0.00000
SCALE2 0.000000 0.013931 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014041 0.00000