PDB Short entry for 4UDW HEADER HYDROLASE 12-DEC-14 4UDW TITLE THROMBIN IN COMPLEX WITH 1-(2R)-2-AMINO-3-PHENYL-PROPANOYL-N-(2, TITLE 2 5DICHLOROPHENYL)METHYLPYRROLIDINE-2-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-620; COMPND 5 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 6 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN ALPHA; COMPND 7 EC: 3.4.21.5; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HIRUDIN VARIANT-2; COMPND 10 CHAIN: I; COMPND 11 FRAGMENT: UNP RESIDUES 62-72; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: HIRUDIN (54-65) (SULFATED); COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 16 CHAIN: L; COMPND 17 FRAGMENT: THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360; COMPND 18 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 19 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN ALPHA; COMPND 20 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 6 20-DEC-23 4UDW 1 HETSYN REVDAT 5 29-JUL-20 4UDW 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 23-OCT-19 4UDW 1 LINK ATOM REVDAT 3 07-MAR-18 4UDW 1 REMARK REVDAT 2 23-SEP-15 4UDW 1 JRNL REVDAT 1 26-AUG-15 4UDW 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. 1.16 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 116082 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 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 : 5801 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 71.2647 - 3.6038 0.99 3853 203 0.1412 0.1352 REMARK 3 2 3.6038 - 2.8604 0.99 3805 201 0.1405 0.1484 REMARK 3 3 2.8604 - 2.4988 0.99 3758 197 0.1320 0.1516 REMARK 3 4 2.4988 - 2.2703 0.99 3773 199 0.1191 0.1535 REMARK 3 5 2.2703 - 2.1076 0.99 3790 199 0.1121 0.1280 REMARK 3 6 2.1076 - 1.9833 1.00 3745 198 0.1095 0.1336 REMARK 3 7 1.9833 - 1.8840 1.00 3824 201 0.1044 0.1324 REMARK 3 8 1.8840 - 1.8020 1.00 3799 200 0.1019 0.1310 REMARK 3 9 1.8020 - 1.7326 0.99 3704 195 0.0948 0.1190 REMARK 3 10 1.7326 - 1.6728 0.99 3764 198 0.0895 0.1117 REMARK 3 11 1.6728 - 1.6205 0.99 3737 197 0.0888 0.1111 REMARK 3 12 1.6205 - 1.5742 0.99 3753 197 0.0898 0.1117 REMARK 3 13 1.5742 - 1.5327 0.99 3734 196 0.0885 0.1207 REMARK 3 14 1.5327 - 1.4953 0.99 3726 196 0.0938 0.1144 REMARK 3 15 1.4953 - 1.4613 0.98 3707 195 0.0990 0.1401 REMARK 3 16 1.4613 - 1.4302 0.98 3720 196 0.1035 0.1459 REMARK 3 17 1.4302 - 1.4016 0.98 3693 194 0.1111 0.1356 REMARK 3 18 1.4016 - 1.3752 0.98 3723 196 0.1165 0.1483 REMARK 3 19 1.3752 - 1.3506 0.98 3678 194 0.1197 0.1320 REMARK 3 20 1.3506 - 1.3277 0.98 3694 194 0.1287 0.1699 REMARK 3 21 1.3277 - 1.3063 0.98 3690 193 0.1318 0.1458 REMARK 3 22 1.3063 - 1.2862 0.98 3680 194 0.1370 0.1523 REMARK 3 23 1.2862 - 1.2673 0.97 3654 192 0.1442 0.1675 REMARK 3 24 1.2673 - 1.2494 0.97 3651 192 0.1527 0.1818 REMARK 3 25 1.2494 - 1.2325 0.96 3679 193 0.1681 0.1837 REMARK 3 26 1.2325 - 1.2165 0.94 3521 185 0.1761 0.1863 REMARK 3 27 1.2165 - 1.2013 0.93 3496 185 0.1894 0.2378 REMARK 3 28 1.2013 - 1.1868 0.90 3398 178 0.2033 0.2239 REMARK 3 29 1.1868 - 1.1730 0.88 3347 177 0.2158 0.2264 REMARK 3 30 1.1730 - 1.1599 0.86 3185 166 0.2207 0.2388 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 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 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 : 0.012 2573 REMARK 3 ANGLE : 1.506 3497 REMARK 3 CHIRALITY : 0.092 365 REMARK 3 PLANARITY : 0.009 451 REMARK 3 DIHEDRAL : 15.499 1024 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: DISORDERED REGIONS WERE NOT MODELED REMARK 4 REMARK 4 4UDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062558. 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 : 116096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 71.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.02000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 (%): 49.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 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 34.82000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.82000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.55300 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: 4240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.5 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 375 HOH H2096 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 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 148 REMARK 465 LYS H 149 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 SER H 36A OG REMARK 470 LYS H 110 CD CE NZ REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 186D CE NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 LYS H 240 CE NZ REMARK 470 ASP I 555 OD1 OD2 REMARK 470 GLU I 558 CG CD OE1 OE2 REMARK 470 GLU I 561 CG CD OE1 OE2 REMARK 470 GLN I 565 CD OE1 NE2 REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 9 CD 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 564 O - C - N ANGL. DEV. = -16.7 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 84.29 -153.61 REMARK 500 ASN H 60G 82.64 -158.40 REMARK 500 HIS H 71 -64.22 -131.87 REMARK 500 ILE H 79 -60.20 -125.33 REMARK 500 PHE L 7 -90.32 -128.96 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 564 -23.40 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 H1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 81.8 REMARK 620 3 HOH H2204 O 65.8 72.9 REMARK 620 4 HOH H2205 O 86.9 168.7 102.6 REMARK 620 5 HOH H2209 O 172.7 94.1 107.3 97.2 REMARK 620 N 1 2 3 4 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 95.6 REMARK 620 3 HOH H2225 O 160.8 70.1 REMARK 620 4 HOH H2227 O 85.5 90.5 82.0 REMARK 620 5 HOH H2235 O 100.0 85.0 91.7 173.2 REMARK 620 6 HOH H2253 O 105.4 157.5 87.6 83.4 98.8 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: 4UD9 RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 5-CHLOROTHIOPHENE-2-CARBOXAMIDE REMARK 900 RELATED ID: 4UDH RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 4-METHOXY-N-(2-PYRIDINYL) BENZAMIDE 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 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON REMARK 999 DESITY REMARK 999 GLY 554 WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY DBREF 4UDW H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 4UDW I 555 565 UNP P09945 HIRV2_HIRME 62 72 DBREF 4UDW L 1C 14K UNP P00734 THRB_HUMAN 333 360 SEQRES 1 H 258 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 258 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 258 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 258 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 258 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 258 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 258 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 258 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 258 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 258 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 258 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 258 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 I 11 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 4UDW ASN H 60G ASN GLYCOSYLATION SITE MODRES 4UDW TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NA H1247 1 HET NA H1248 1 HET N6L H1249 28 HET PO4 H1250 5 HET GOL H1251 6 HET NAG H1252 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM N6L D-PHENYLALANYL-N-(2,5-DICHLOROBENZYL)-L-PROLINAMIDE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL 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 N6L C21 H23 CL2 N3 O2 FORMUL 7 PO4 O4 P 3- FORMUL 8 GOL C3 H8 O3 FORMUL 9 NAG C8 H15 N O6 FORMUL 10 HOH *309(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 2.05 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H1252 1555 1555 1.41 LINK C GLU I 562 N TYS I 563 1555 1555 1.33 LINK C TYS I 563 N LEU I 564 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 2.34 LINK O ARG H 221A NA NA H1247 1555 1555 2.28 LINK O LYS H 224 NA NA H1247 1555 1555 2.36 LINK NA NA H1247 O HOH H2225 1555 1555 2.46 LINK NA NA H1247 O HOH H2227 1555 1555 2.69 LINK NA NA H1247 O HOH H2235 1555 1555 2.33 LINK NA NA H1247 O HOH H2253 1555 1555 2.39 LINK NA NA H1248 O HOH H2204 1555 1555 2.91 LINK NA NA H1248 O HOH H2205 1555 1555 2.43 LINK NA NA H1248 O HOH H2209 1555 1555 2.37 CISPEP 1 SER H 36A PRO H 37 0 -3.02 CRYST1 69.640 71.106 72.327 90.00 100.44 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 0.014360 0.000000 0.002646 0.00000 SCALE2 0.000000 0.014064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014059 0.00000