PDB Short entry for 1A46 HEADER HYDROLASE/HYDROLASE INHIBITOR 11-FEB-98 1A46 TITLE THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC 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 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; SOURCE 14 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 15 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 16 ORGANISM_TAXID: 6421 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 5 02-AUG-23 1A46 1 REMARK LINK REVDAT 4 13-JUL-11 1A46 1 VERSN REVDAT 3 24-FEB-09 1A46 1 VERSN REVDAT 2 01-APR-03 1A46 1 JRNL REVDAT 1 27-MAY-98 1A46 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. 2.12 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) : 2.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 3 NUMBER OF REFLECTIONS : 15585 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) : 0.155 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 : 2298 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 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) : 0.020 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.042 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.049 ; 0.045 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.028 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.190 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.220 ; 0.600 REMARK 3 MULTIPLE TORSION (A) : 0.260 ; 0.600 REMARK 3 H-BOND (X...Y) (A) : 0.250 ; 0.600 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) : 21.000; 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) : 1.000 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.500 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A46 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_1000170370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18219 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.120 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PREVIOUS STRUCTURE REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1HAH 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: 0.1 M SODIUM PHOSPHATE BUFFER, PH 7.3, REMARK 280 27-28 % PEG 8000, HANGING DROPS AND MACROSEEDING; THEN SOAKED IN REMARK 280 PEG-PHOSPHATE-0.1 M NACL, AND THE MOL 106 INHIBITOR WAS ADDED IN REMARK 280 3 STEPS WITH FINAL CONC. 7.3 MM, VAPOR DIFFUSION - HANGING DROP REMARK 280 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 35.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.54500 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 00K 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 ALA L 1B 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 LYS L 14A CD CE NZ REMARK 470 LYS H 110 CB CG CD CE NZ REMARK 470 LYS H 186D CG CD CE NZ REMARK 470 LYS H 236 CB CG CD CE NZ REMARK 470 ASP I 355 CB CG OD1 OD2 REMARK 470 GLU I 358 CB CG CD OE1 OE2 REMARK 470 GLU I 361 CB CG CD OE1 OE2 REMARK 470 GLU I 362 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 O ILE H 242 O GLY H 246 2.13 REMARK 500 O HOH H 403 O HOH H 465 2.19 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 2.02 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 ASP L 1A CB - CG - OD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG L 14D NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG H 35 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR H 60A CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLU H 61 CA - CB - CG ANGL. DEV. = 18.6 DEGREES REMARK 500 GLU H 61 CB - CG - CD ANGL. DEV. = 26.0 DEGREES REMARK 500 GLU H 61 CG - CD - OE1 ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG H 67 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG H 93 CD - NE - CZ ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG H 97 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP H 116 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG H 126 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 TYR H 134 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 GLU H 164 CG - CD - OE1 ANGL. DEV. = -13.4 DEGREES REMARK 500 GLU H 164 CG - CD - OE2 ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG H 165 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG H 173 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG H 175 CD - NE - CZ ANGL. DEV. = -10.1 DEGREES REMARK 500 TYR H 184A CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP H 189 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 CYS H 191 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 GLU H 192 OE1 - CD - OE2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ASN H 205 OD1 - CG - ND2 ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG H 221A NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 GLY H 246 CA - C - O ANGL. DEV. = -13.2 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 PHE L 7 -81.66 -127.18 REMARK 500 SER H 36A 120.05 173.30 REMARK 500 TYR H 60A 86.49 -159.22 REMARK 500 ASN H 60G 76.57 -151.50 REMARK 500 HIS H 71 -50.08 -125.33 REMARK 500 GLU H 77 73.19 -68.98 REMARK 500 ASN H 78 -8.93 85.07 REMARK 500 ILE H 79 -60.50 -106.54 REMARK 500 GLU H 97A -62.71 -122.74 REMARK 500 SER H 195 146.61 -35.28 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 549 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 85.9 REMARK 620 3 PHE H 204A O 96.1 98.8 REMARK 620 4 HOH H 468 O 86.0 170.1 87.7 REMARK 620 5 HOH H 529 O 171.4 93.4 92.5 93.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 548 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 92.1 REMARK 620 3 HOH H 416 O 151.6 67.1 REMARK 620 4 HOH H 443 O 84.0 83.2 74.9 REMARK 620 5 HOH H 530 O 101.2 80.7 94.4 163.3 REMARK 620 6 HOH H 531 O 114.5 151.5 84.4 89.2 102.7 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-N-[(2R,3S)-7-AMINO-1- REMARK 630 (CYCLOHEXYLAMINO)-2-HYDROXY-1-OXOHEPTAN-3-YL]-7-BENZYL-8- REMARK 630 OXOHEXAHYDRO-1H-PYRAZOLO[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 00K H 372 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: 00U 00V ANL REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 548 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 549 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 00K 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 1A46 L 1H 14N UNP P00734 THRB_HUMAN 328 363 DBREF 1A46 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1A46 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 1A46 TYS I 363 TYR O-SULFO-L-TYROSINE HET TYS I 363 16 HET NA H 548 1 HET NA H 549 1 HET 00K H 372 38 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM 00K (1S,7S)-7-AMINO-N-[(2R,3S)-7-AMINO-1-(CYCLOHEXYLAMINO)- HETNAM 2 00K 2-HYDROXY-1-OXOHEPTAN-3-YL]-7-BENZYL-8-OXOHEXAHYDRO- HETNAM 3 00K 1H-PYRAZOLO[1,2-A]PYRIDAZINE-1-CARBOXAMIDE HETSYN 00K MOL-106 FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 00K C28 H44 N6 O4 FORMUL 7 HOH *165(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 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 LINK OG SER H 195 C 00K H 372 1555 1555 1.78 LINK C GLU I 362 N TYS I 363 1555 1555 1.33 LINK C TYS I 363 N LEU I 364 1555 1555 1.34 LINK O LYS H 169 NA NA H 549 1555 1555 2.38 LINK O THR H 172 NA NA H 549 1555 1555 2.24 LINK O PHE H 204A NA NA H 549 4546 1555 2.45 LINK O ARG H 221A NA NA H 548 1555 1555 2.36 LINK O LYS H 224 NA NA H 548 1555 1555 2.46 LINK O HOH H 416 NA NA H 548 1555 1555 2.70 LINK O HOH H 443 NA NA H 548 1555 1555 2.90 LINK O HOH H 468 NA NA H 549 1555 1555 2.39 LINK O HOH H 529 NA NA H 549 1555 1555 2.30 LINK O HOH H 530 NA NA H 548 1555 1555 2.11 LINK O HOH H 531 NA NA H 548 1555 1555 2.51 CISPEP 1 SER H 36A PRO H 37 0 -0.84 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H 416 HOH H 443 SITE 2 AC1 6 HOH H 530 HOH H 531 SITE 1 AC2 5 LYS H 169 THR H 172 PHE H 204A HOH H 468 SITE 2 AC2 5 HOH H 529 SITE 1 AC3 17 LEU H 41 HIS H 57 TYR H 60A TRP H 60D SITE 2 AC3 17 GLU H 97A ASP H 189 ALA H 190 GLU H 192 SITE 3 AC3 17 GLY H 193 ASP H 194 SER H 195 SER H 214 SITE 4 AC3 17 TRP H 215 GLY H 216 GLY H 219 HOH H 425 SITE 5 AC3 17 HOH H 466 SITE 1 AC4 12 PHE H 34 LYS H 36 GLN H 38 ARG H 73 SITE 2 AC4 12 THR H 74 ARG H 75 TYR H 76 LYS H 81 SITE 3 AC4 12 ILE H 82 MET H 84 HOH H 470 HOH I 522 CRYST1 71.300 73.090 73.820 90.00 101.12 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 0.014025 0.000000 0.002757 0.00000 SCALE2 0.000000 0.013682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013806 0.00000