HEADER HYDROLASE/HYDROLASE INHIBITOR 05-MAR-98 1A61
TITLE THROMBIN COMPLEXED WITH A BETA-MIMETIC THIAZOLE-CONTAINING INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-THROMBIN (SMALL SUBUNIT);
COMPND 3 CHAIN: L;
COMPND 4 EC: 3.4.21.5;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: ALPHA-THROMBIN (LARGE SUBUNIT);
COMPND 7 CHAIN: H;
COMPND 8 EC: 3.4.21.5;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: HIRUGEN;
COMPND 11 CHAIN: I;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 ORGAN: BLOOD;
SOURCE 6 TISSUE: BLOOD;
SOURCE 7 MOL_ID: 2;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_COMMON: HUMAN;
SOURCE 10 ORGANISM_TAXID: 9606;
SOURCE 11 ORGAN: BLOOD;
SOURCE 12 TISSUE: BLOOD;
SOURCE 13 MOL_ID: 3
KEYWDS COMPLEX (SERINE PROTEASE-INHIBITOR), HYDROLASE-HYDROLASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR R.ST CHARLES,J.H.MATTHEWS,E.ZHANG,A.TULINSKY,M.KAHN
REVDAT 6 23-OCT-24 1A61 1 REMARK
REVDAT 5 05-JUN-24 1A61 1 COMPND REMARK HETNAM LINK
REVDAT 4 13-JUL-11 1A61 1 VERSN
REVDAT 3 24-FEB-09 1A61 1 VERSN
REVDAT 2 01-APR-03 1A61 1 JRNL
REVDAT 1 17-JUN-98 1A61 0
JRNL AUTH R.ST CHARLES,J.H.MATTHEWS,E.ZHANG,A.TULINSKY
JRNL TITL BOUND STRUCTURES OF NOVEL P3-P1' BETA-STRAND MIMETIC
JRNL TITL 2 INHIBITORS OF THROMBIN.
JRNL REF J.MED.CHEM. V. 42 1376 1999
JRNL REFN ISSN 0022-2623
JRNL PMID 10212123
JRNL DOI 10.1021/JM980052N
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
REMARK 1 AUTH 2 A.TULINSKY
REMARK 1 TITL CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
REMARK 1 TITL 2 INHIBITORS: PROBES OF THE S1' BINDING SITE
REMARK 1 REF BIOPHYS.J. V. 71 2830 1996
REMARK 1 REFN ISSN 0006-3495
REMARK 1 REFERENCE 2
REMARK 1 AUTH T.P.WU,V.YEE,A.TULINSKY,R.A.CHRUSCIEL,H.NAKANISHI,R.SHEN,
REMARK 1 AUTH 2 C.PRIEBE,M.KAHN
REMARK 1 TITL THE STRUCTURE OF A DESIGNED PEPTIDOMIMETIC INHIBITOR COMPLEX
REMARK 1 TITL 2 OF ALPHA-THROMBIN
REMARK 1 REF PROTEIN ENG. V. 6 471 1993
REMARK 1 REFN ISSN 0269-2139
REMARK 1 REFERENCE 3
REMARK 1 AUTH A.TULINSKY,X.QIU
REMARK 1 TITL ACTIVE SITE AND EXOSITE BINDING OF ALPHA-THROMBIN
REMARK 1 REF BLOOD COAGULATION V. 4 305 1993
REMARK 1 REF 2 FIBRINOLYSIS
REMARK 1 REFN ISSN 0957-5235
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROFFT
REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 76.0
REMARK 3 NUMBER OF REFLECTIONS : 13643
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.148
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2333
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 38
REMARK 3 SOLVENT ATOMS : 141
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.015 ; 0.018
REMARK 3 ANGLE DISTANCE (A) : 0.050 ; 0.038
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.064 ; 0.058
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.037 ; 0.040
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.180 ; 0.150
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : 0.240 ; 0.500
REMARK 3 MULTIPLE TORSION (A) : 0.300 ; 0.500
REMARK 3 H-BOND (X...Y) (A) : 0.300 ; 0.500
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : 4.000 ; 3.000
REMARK 3 STAGGERED (DEGREES) : 22.000; 15.000
REMARK 3 TRANSVERSE (DEGREES) : 30.000; 20.000
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.800 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.600 ; 2.500
REMARK 3 SIDE-CHAIN BOND (A**2) : 3.200 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.400 ; 3.500
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1A61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170436.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-JUL-95
REMARK 200 TEMPERATURE (KELVIN) : 298
REMARK 200 PH : 7.3
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 RUH2R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : R-AXIS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14517
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 60.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 77.0
REMARK 200 DATA REDUNDANCY : 2.400
REMARK 200 R MERGE (I) : 0.05200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> 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) : 2.27
REMARK 200 COMPLETENESS FOR SHELL (%) : 54.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.14700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: THROMBIN-HIRUGEN WAS CRYSTALLIZED FROM
REMARK 280 0.1 M SODIUM PHOSPHATE BUFFER AT PH 7.3, 28% PEG 8000 IN HANGING
REMARK 280 DROPS WITH MACROSEEDING. THE MOL 127 INHIBITOR WAS ADDED BY
REMARK 280 SOAKING., VAPOR DIFFUSION - HANGING DROP AND MACROSEEDING
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 35.42500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.20500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.42500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.20500
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 APPLY THE FOLLOWING TO CHAINS: L, H, 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 400
REMARK 400 COMPOUND
REMARK 400 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L*
REMARK 400 IS USED FOR RESIDUES 1H - 15 AND CHAIN IDENTIFIER *H* IS USED FOR
REMARK 400 RESIDUES 16 - 247. CHAIN IDENTIFIER *I* IS USED FOR HIRUGEN, THE
REMARK 400 CARBOXYL TERMINUS OF HIRUDIN, WHICH OCCUPIES THE EXOSITE. THE
REMARK 400 INHIBITOR 00N IS COVALENTLY CONNECTED TO SER 195 OF THE ENZYME TO
REMARK 400 FORM A HEMIKETAL.
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 L 1H
REMARK 465 PHE L 1G
REMARK 465 GLY L 1F
REMARK 465 SER L 1E
REMARK 465 GLY L 1D
REMARK 465 GLU L 1C
REMARK 465 ASP L 14L
REMARK 465 GLY L 14M
REMARK 465 ARG L 14N
REMARK 465 THR H 146A
REMARK 465 TRP H 146B
REMARK 465 THR H 146C
REMARK 465 ALA H 146D
REMARK 465 ASN H 146E
REMARK 465 VAL H 146F
REMARK 465 GLY H 146G
REMARK 465 LYS H 146H
REMARK 465 GLU H 247
REMARK 465 ASN I 353
REMARK 465 GLY I 354
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 GLU I 361 CB CG CD OE1 OE2
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 NH1 ARG L 14D OE2 GLU L 14H 2.16
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 NH1 ARG H 75 OE1 GLU I 357 2555 2.12
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 ARG L 4 NE - CZ - NH2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 ASP L 14 CB - CG - OD1 ANGL. DEV. = -8.2 DEGREES
REMARK 500 ASP L 14 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES
REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP H 21 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES
REMARK 500 ARG H 35 CD - NE - CZ ANGL. DEV. = -13.8 DEGREES
REMARK 500 GLN H 38 CB - CG - CD ANGL. DEV. = 18.9 DEGREES
REMARK 500 CYS H 42 CA - CB - SG ANGL. DEV. = 10.4 DEGREES
REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = -7.2 DEGREES
REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ARG H 50 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ARG H 67 NH1 - CZ - NH2 ANGL. DEV. = -8.8 DEGREES
REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 ARG H 75 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ARG H 75 NE - CZ - NH2 ANGL. DEV. = 7.3 DEGREES
REMARK 500 ARG H 77A NE - CZ - NH1 ANGL. DEV. = -7.8 DEGREES
REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES
REMARK 500 TYR H 94 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 ARG H 97 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES
REMARK 500 ARG H 126 CD - NE - CZ ANGL. DEV. = -9.6 DEGREES
REMARK 500 ARG H 126 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES
REMARK 500 ARG H 137 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 GLN H 151 CA - CB - CG ANGL. DEV. = -13.3 DEGREES
REMARK 500 VAL H 154 N - CA - CB ANGL. DEV. = -14.0 DEGREES
REMARK 500 GLU H 164 OE1 - CD - OE2 ANGL. DEV. = -8.7 DEGREES
REMARK 500 GLU H 164 CG - CD - OE2 ANGL. DEV. = 15.0 DEGREES
REMARK 500 ARG H 165 CD - NE - CZ ANGL. DEV. = 27.6 DEGREES
REMARK 500 ARG H 165 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ARG H 173 CD - NE - CZ ANGL. DEV. = -8.9 DEGREES
REMARK 500 ARG H 175 CD - NE - CZ ANGL. DEV. = -9.8 DEGREES
REMARK 500 TYR H 184A CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES
REMARK 500 GLU H 186B OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES
REMARK 500 ARG H 187 CD - NE - CZ ANGL. DEV. = -9.5 DEGREES
REMARK 500 ARG H 187 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES
REMARK 500 ASP H 189 CB - CG - OD2 ANGL. DEV. = 7.9 DEGREES
REMARK 500 GLU H 192 CG - CD - OE2 ANGL. DEV. = 14.2 DEGREES
REMARK 500 GLY H 193 CA - C - O ANGL. DEV. = -11.0 DEGREES
REMARK 500 ASP H 194 CB - CG - OD1 ANGL. DEV. = -10.3 DEGREES
REMARK 500 ARG H 206 NH1 - CZ - NH2 ANGL. DEV. = 7.4 DEGREES
REMARK 500 ARG H 206 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES
REMARK 500 GLU H 217 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES
REMARK 500 TYR H 225 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 ARG H 233 CD - NE - CZ ANGL. DEV. = -12.3 DEGREES
REMARK 500 ARG H 233 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES
REMARK 500 ASP H 243 CB - CA - C ANGL. DEV. = 14.8 DEGREES
REMARK 500 ASP H 243 CA - CB - CG ANGL. DEV. = 22.4 DEGREES
REMARK 500 ASP H 243 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 53 ANGLE DEVIATIONS.
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 L 7 -84.03 -125.00
REMARK 500 TYR L 14J 56.85 -91.10
REMARK 500 GLU H 39 147.23 -178.71
REMARK 500 ALA H 44 -173.39 -170.35
REMARK 500 ARG H 50 -5.84 -148.66
REMARK 500 TYR H 60A 85.52 -155.85
REMARK 500 ASN H 78 -7.66 83.57
REMARK 500 LEU H 99 35.62 80.02
REMARK 500 SER H 115 -173.59 -170.86
REMARK 500 LYS H 186D 135.02 -170.53
REMARK 500 SER H 195 142.22 -34.07
REMARK 500 SER H 214 -61.90 -121.27
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 TYR H 89 0.07 SIDE CHAIN
REMARK 500 ASN H 98 0.07 SIDE CHAIN
REMARK 500 GLN H 156 0.07 SIDE CHAIN
REMARK 500 PHE H 232 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 LEU L 3 11.80
REMARK 500 PRO L 5 -20.11
REMARK 500 SER H 20 10.29
REMARK 500 PHE H 60H -15.53
REMARK 500 ASN H 62 12.36
REMARK 500 GLU H 80 11.23
REMARK 500 LYS H 87 -11.08
REMARK 500 HIS H 91 10.06
REMARK 500 ASN H 98 13.65
REMARK 500 HIS H 119 -11.57
REMARK 500 TYR H 134 -10.32
REMARK 500 LEU H 160 -12.23
REMARK 500 PRO H 161 10.10
REMARK 500 MET H 180 13.18
REMARK 500 ILE H 212 11.52
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 H 651 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS H 169 O
REMARK 620 2 THR H 172 O 87.6
REMARK 620 3 PHE H 204A O 98.6 107.6
REMARK 620 4 HOH H 558 O 83.5 158.9 92.7
REMARK 620 5 HOH H 559 O 167.2 95.1 92.5 89.6
REMARK 620 6 HOH H 560 O 74.1 73.1 172.7 86.0 94.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA H 650 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG H 221A O
REMARK 620 2 LYS H 224 O 104.3
REMARK 620 3 HOH H 429 O 157.8 74.7
REMARK 620 4 HOH H 476 O 98.7 156.1 81.6
REMARK 620 5 HOH H 496 O 91.9 86.1 65.9 86.9
REMARK 620 6 HOH H 561 O 96.2 93.6 106.0 90.1 171.7
REMARK 620 N 1 2 3 4 5
REMARK 630
REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR
REMARK 630 MOLECULE NAME: (1S,7S)-7-AMINO-7-BENZYL-N-{(1S)-4-CARBAMIMIDAMIDO-
REMARK 630 1-[(S)-HYDROXY(1,3-THIAZOL-2-YL)METHYL]BUTYL}-8-OXOHEXAHYDRO-1H-
REMARK 630 PYRA ZOLO[1,2-A]PYRIDAZINE-1-CARBOXAMIDE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 00N H 372
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: 00U 00Y
REMARK 630 DETAILS: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: NULL
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 650
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 651
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 00N H 372
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUGEN
DBREF 1A61 L 1H 14N UNP P00734 THRB_HUMAN 328 363
DBREF 1A61 H 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 1A61 I 353 364 UNP P09945 ITH3_HIRME 60 71
SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO
SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG
SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG
SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO
SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU
SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU
SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS
SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE
SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS
SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO
SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU
SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN
SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU
SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR
SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY
SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO
SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN
SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP
SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS
SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU
SEQRES 1 I 12 ASN GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU
MODRES 1A61 TYS I 363 TYR O-SULFO-L-TYROSINE
HET TYS I 363 16
HET NA H 650 1
HET NA H 651 1
HET 00N H 372 36
HETNAM TYS O-SULFO-L-TYROSINE
HETNAM NA SODIUM ION
HETNAM 00N (1S,7S)-7-AMINO-7-BENZYL-N-{(1S)-4-CARBAMIMIDAMIDO-1-
HETNAM 2 00N [(S)-HYDROXY(1,3-THIAZOL-2-YL)METHYL]BUTYL}-8-
HETNAM 3 00N OXOHEXAHYDRO-1H-PYRA ZOLO[1,2-A]PYRIDAZINE-1-
HETNAM 4 00N CARBOXAMIDE
HETSYN 00N MOL-127
FORMUL 3 TYS C9 H11 N O6 S
FORMUL 4 NA 2(NA 1+)
FORMUL 6 00N C24 H34 N8 O3 S
FORMUL 7 HOH *141(H2 O)
HELIX 1 H1 ALA H 55 LEU H 60 1 6
HELIX 2 H2 GLU H 164 SER H 171 1 8
HELIX 3 H3 ASP H 125 LEU H 129C 1 8
HELIX 4 H4 VAL H 231 GLN H 244 1 14
SHEET 1 B1 7 PRO H 28 ARG H 35 0
SHEET 2 B1 7 CYS H 42 ASP H 49 -1
SHEET 3 B1 7 ARG H 50 ALA H 56 -1
SHEET 4 B1 7 ARG H 101 LYS H 110 -1
SHEET 5 B1 7 LYS H 81 PRO H 92 -1
SHEET 6 B1 7 ASP H 63 GLY H 69 -1
SHEET 7 B1 7 PRO H 28 ARG H 35 -1
SHEET 1 B2 7 GLY H 133 TRP H 141 0
SHEET 2 B2 7 LEU H 155 ILE H 162 -1
SHEET 3 B2 7 ASN H 179 PRO H 186 -1
SHEET 4 B2 7 GLY H 223 THR H 229 -1
SHEET 5 B2 7 ILE H 212 GLU H 217 -1
SHEET 6 B2 7 GLY H 193 MET H 201 -1
SHEET 7 B2 7 GLY H 133 TRP H 141 -1
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.01
SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.02
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.02
LINK OG SER H 195 C 00N H 372 1555 1555 1.80
LINK C GLU I 362 N TYS I 363 1555 1555 1.31
LINK C TYS I 363 N LEU I 364 1555 1555 1.33
LINK O LYS H 169 NA NA H 651 1555 1555 2.55
LINK O THR H 172 NA NA H 651 1555 1555 2.22
LINK O PHE H 204A NA NA H 651 4546 1555 2.10
LINK O ARG H 221A NA NA H 650 1555 1555 2.38
LINK O LYS H 224 NA NA H 650 1555 1555 2.32
LINK O HOH H 429 NA NA H 650 1555 1555 2.40
LINK O HOH H 476 NA NA H 650 1555 1555 2.84
LINK O HOH H 496 NA NA H 650 1555 1555 3.14
LINK O HOH H 558 NA NA H 651 1555 1555 2.49
LINK O HOH H 559 NA NA H 651 1555 1555 2.32
LINK O HOH H 560 NA NA H 651 1555 1555 2.69
LINK O HOH H 561 NA NA H 650 1555 1555 2.12
CISPEP 1 SER H 36A PRO H 37 0 1.37
SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195
SITE 1 AC1 5 ARG H 221A LYS H 224 HOH H 429 HOH H 476
SITE 2 AC1 5 HOH H 561
SITE 1 AC2 6 LYS H 169 THR H 172 PHE H 204A HOH H 558
SITE 2 AC2 6 HOH H 559 HOH H 560
SITE 1 AC3 17 HIS H 57 TYR H 60A TRP H 60D LYS H 60F
SITE 2 AC3 17 GLU H 97A ASP H 189 ALA H 190 GLY H 193
SITE 3 AC3 17 ASP H 194 SER H 195 SER H 214 TRP H 215
SITE 4 AC3 17 GLY H 216 GLY H 219 GLY H 226 HOH H 401
SITE 5 AC3 17 HOH H 435
SITE 1 AC4 19 PHE H 34 LYS H 36 LEU H 65 ARG H 73
SITE 2 AC4 19 THR H 74 ARG H 75 TYR H 76 GLU H 80
SITE 3 AC4 19 LYS H 81 ILE H 82 MET H 84 SER H 153
SITE 4 AC4 19 HOH H 482 HOH I 454 HOH I 474 HOH I 488
SITE 5 AC4 19 HOH I 492 HOH I 523 HOH I 538
CRYST1 70.850 72.410 72.970 90.00 101.00 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 0.014114 0.000000 0.002744 0.00000
SCALE2 0.000000 0.013810 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013961 0.00000