HEADER HYDROLASE 09-DEC-14 4UD9 TITLE THROMBIN IN COMPLEX WITH 5-CHLOROTHIOPHENE-2-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-622; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HIRUDIN-2; COMPND 8 CHAIN: I; COMPND 9 SYNONYM: HIRUDIN II; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: HIRUDIN (54-65) (SULFATED); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PROTHROMBIN; COMPND 14 CHAIN: L; COMPND 15 FRAGMENT: THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360; COMPND 16 SYNONYM: COAGULATION FACTOR II; COMPND 17 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: PURIFIED FROM HUMAN BLOOD PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 9 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 10 ORGANISM_TAXID: 6421; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: PURIFIED FROM HUMAN BLOOD PLASMA KEYWDS HYDROLASE, HYDROLASE INHIBITOR COMPLEX, SERINE PROTEASE, BLOOD KEYWDS 2 COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 3 BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, FRAGMENT, KEYWDS 4 GLYCOSYLATION, BLOOD EXPDTA X-RAY DIFFRACTION AUTHOR E.RUEHMANN,A.HEINE,G.KLEBE REVDAT 7 31-JAN-24 4UD9 1 REMARK REVDAT 6 07-DEC-22 4UD9 1 COMPND SOURCE REMARK DBREF REVDAT 6 2 1 SEQRES HETSYN LINK ATOM REVDAT 5 29-JUL-20 4UD9 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 23-OCT-19 4UD9 1 LINK ATOM REVDAT 3 07-MAR-18 4UD9 1 REMARK REVDAT 2 23-SEP-15 4UD9 1 JRNL REVDAT 1 26-AUG-15 4UD9 0 JRNL AUTH E.RUEHMANN,M.BETZ,A.HEINE,G.KLEBE JRNL TITL FRAGMENTS CAN BIND EITHER MORE ENTHALPY OR ENTROPY-DRIVEN: JRNL TITL 2 CRYSTAL STRUCTURES AND RESIDUAL HYDRATION PATTERN SUGGEST JRNL TITL 3 WHY. JRNL REF J.MED.CHEM. V. 58 6960 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26270568 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00812 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 127834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.6990 - 3.4928 1.00 4284 225 0.1439 0.1638 REMARK 3 2 3.4928 - 2.7727 1.00 4199 221 0.1425 0.1617 REMARK 3 3 2.7727 - 2.4223 1.00 4217 222 0.1335 0.1483 REMARK 3 4 2.4223 - 2.2008 1.00 4200 221 0.1212 0.1157 REMARK 3 5 2.2008 - 2.0431 1.00 4212 222 0.1115 0.1122 REMARK 3 6 2.0431 - 1.9227 1.00 4140 218 0.1140 0.1205 REMARK 3 7 1.9227 - 1.8264 1.00 4210 221 0.1106 0.1287 REMARK 3 8 1.8264 - 1.7469 1.00 4165 219 0.1044 0.1231 REMARK 3 9 1.7469 - 1.6796 1.00 4162 219 0.1021 0.1272 REMARK 3 10 1.6796 - 1.6217 1.00 4178 220 0.1001 0.1204 REMARK 3 11 1.6217 - 1.5710 1.00 4159 219 0.0977 0.1166 REMARK 3 12 1.5710 - 1.5261 1.00 4163 219 0.0956 0.1031 REMARK 3 13 1.5261 - 1.4859 1.00 4194 221 0.0992 0.1131 REMARK 3 14 1.4859 - 1.4496 1.00 4156 219 0.0990 0.1370 REMARK 3 15 1.4496 - 1.4167 0.99 4172 219 0.1041 0.1293 REMARK 3 16 1.4167 - 1.3865 1.00 4109 217 0.1060 0.1224 REMARK 3 17 1.3865 - 1.3588 0.99 4182 220 0.1085 0.1450 REMARK 3 18 1.3588 - 1.3331 0.99 4151 218 0.1135 0.1397 REMARK 3 19 1.3331 - 1.3093 0.99 4123 217 0.1160 0.1408 REMARK 3 20 1.3093 - 1.2871 1.00 4145 218 0.1191 0.1439 REMARK 3 21 1.2871 - 1.2664 0.99 4170 220 0.1227 0.1510 REMARK 3 22 1.2664 - 1.2469 0.99 4108 216 0.1304 0.1470 REMARK 3 23 1.2469 - 1.2286 0.99 4139 218 0.1343 0.1478 REMARK 3 24 1.2286 - 1.2112 0.97 4068 214 0.1427 0.1649 REMARK 3 25 1.2112 - 1.1949 0.96 3994 210 0.1545 0.1730 REMARK 3 26 1.1949 - 1.1794 0.96 4020 212 0.1609 0.1902 REMARK 3 27 1.1794 - 1.1646 0.93 3871 204 0.1657 0.1897 REMARK 3 28 1.1646 - 1.1506 0.90 3761 198 0.1700 0.1757 REMARK 3 29 1.1506 - 1.1372 0.87 3586 188 0.1885 0.2208 REMARK 3 30 1.1372 - 1.1244 0.53 2205 116 0.2174 0.1944 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.10 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2589 REMARK 3 ANGLE : 1.380 3503 REMARK 3 CHIRALITY : 0.082 364 REMARK 3 PLANARITY : 0.008 452 REMARK 3 DIHEDRAL : 15.230 1022 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290059778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127839 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 35.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1H8D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEE MATERIALS AND METHODS SECTION OF REMARK 280 PUBLICATION, PH 7.5 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 35.05650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.68100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.05650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.68100 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.5 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 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 H 75 LIES ON A SPECIAL POSITION. 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 ASN H 149B REMARK 465 VAL H 149C REMARK 465 GLY H 149D REMARK 465 LYS H 149E 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 H 107 CE NZ REMARK 470 LYS H 110 CD CE NZ REMARK 470 LYS H 145 CE NZ REMARK 470 THR H 149 OG1 CG2 REMARK 470 LYS H 169 NZ REMARK 470 LYS H 186D NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 LYS H 240 CE NZ REMARK 470 GLN H 244 CG CD OE1 NE2 REMARK 470 GLU H 247 CA C O CB CG CD OE1 REMARK 470 GLU H 247 OE2 REMARK 470 ASP I 518 CG OD1 OD2 REMARK 470 GLU I 521 CG CD OE1 OE2 REMARK 470 GLU I 524 CG CD OE1 OE2 REMARK 470 GLN I 528 CG CD OE1 NE2 REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 14A CE NZ 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 LEU I 527 O - C - N ANGL. DEV. = -22.5 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 TYR H 60A 84.97 -154.50 REMARK 500 ASN H 60G 79.30 -158.62 REMARK 500 HIS H 71 -62.93 -131.19 REMARK 500 ILE H 79 -62.21 -127.28 REMARK 500 GLU H 97A -72.77 -117.95 REMARK 500 PHE L 7 -91.18 -129.88 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 I 527 -29.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 5-CHLORO-2-THIOPHENECARBOXAMIDE (FQI): CAS 22353-82-8 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 H1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 82.3 REMARK 620 3 HOH H2185 O 69.5 79.4 REMARK 620 N 1 2 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 LYS H 224 O 95.3 REMARK 620 3 HOH H2202 O 161.4 70.4 REMARK 620 4 HOH H2203 O 86.9 92.4 82.2 REMARK 620 5 HOH H2212 O 99.4 84.8 91.2 173.3 REMARK 620 6 HOH H2235 O 105.0 159.0 88.6 83.3 97.1 REMARK 620 N 1 2 3 4 5 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UDH RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 4-METHOXY-N-(2-PYRIDINYL) BENZAMIDE REMARK 900 RELATED ID: 4UDW RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 1-(2R)-2-AMINO-3-PHENYL- PROPANOYL-N-(2, REMARK 900 5DICHLOROPHENYL)METHYLPYRROLIDINE-2- CARBOXAMIDE REMARK 900 RELATED ID: 4UE7 RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 1-AMIDINOPIPERIDINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 ASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY REMARK 999 RESIDUES 149B-149E WERE NOT BUILD DUE TO LACK OF ELECTRON REMARK 999 DESITY DBREF 4UD9 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 4UD9 I 517 528 UNP P28504 HIR2_HIRME 54 65 DBREF 4UD9 L 1C 14K UNP P00734 THRB_HUMAN 333 360 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 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN SEQRES 1 L 28 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 L 28 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 L 28 TYR ILE MODRES 4UD9 TYS I 526 TYR MODIFIED RESIDUE HET TYS I 526 16 HET NA H1247 1 HET NA H1248 1 HET PO4 H1249 5 HET DMS H1250 8 HET DMS H1251 8 HET GOL H1252 6 HET GOL H1253 6 HET GOL H1254 6 HET EDO H1255 4 HET EDO H1256 4 HET FQI H1257 9 HET NAG H1258 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM FQI 5-CHLORO-2-THIOPHENECARBOXAMIDE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 PO4 O4 P 3- FORMUL 7 DMS 2(C2 H6 O S) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 12 EDO 2(C2 H6 O2) FORMUL 14 FQI C5 H4 CL N O S FORMUL 15 NAG C8 H15 N O6 FORMUL 16 HOH *291(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 GLY H 246 1 13 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 2.04 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H1258 1555 1555 1.43 LINK C GLU I 525 N TYS I 526 1555 1555 1.33 LINK C TYS I 526 N LEU I 527 1555 1555 1.33 LINK O LYS H 169 NA NA H1248 1555 1555 2.35 LINK O THR H 172 NA NA H1248 1555 1555 2.31 LINK O ARG H 221A NA NA H1247 1555 1555 2.32 LINK O LYS H 224 NA NA H1247 1555 1555 2.37 LINK NA NA H1247 O HOH H2202 1555 1555 2.45 LINK NA NA H1247 O HOH H2203 1555 1555 2.70 LINK NA NA H1247 O HOH H2212 1555 1555 2.34 LINK NA NA H1247 O HOH H2235 1555 1555 2.36 LINK NA NA H1248 O HOH H2185 1555 1555 2.59 CISPEP 1 SER H 36A PRO H 37 0 -4.96 CRYST1 70.113 71.362 72.103 90.00 100.38 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 0.014263 0.000000 0.002613 0.00000 SCALE2 0.000000 0.014013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014100 0.00000