HEADER HYDROLASE 16-MAR-15 4UFD TITLE THROMBIN IN COMPLEX WITH 4-(((1-((2S)-1-((2R)-2-(BENZYLSULFONYLAMINO)- TITLE 2 3-PHENYL-PROPANOYL)PYRROLIDIN-2-YL)-1-OXO-ETHYL)AMINO)METHYL) TITLE 3 BENZAMIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUES 364-621; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HIRUDIN VARIANT-2; COMPND 8 CHAIN: I; COMPND 9 FRAGMENT: RESIDUES 61-72; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: HIRUDIN (54-65) (SULFATED); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 14 CHAIN: L; COMPND 15 FRAGMENT: RESIDUES 333-361; COMPND 16 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, PREORGANIZATION, KEYWDS 4 GLYCOSYLATION, BLOOD EXPDTA X-RAY DIFFRACTION AUTHOR E.RUEHMANN,A.HEINE,G.KLEBE REVDAT 3 29-JUL-20 4UFD 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 02-MAR-16 4UFD 1 JRNL REVDAT 1 27-JAN-16 4UFD 0 JRNL AUTH E.H.RUHMANN,M.RUPP,M.BETZ,A.HEINE,G.KLEBE JRNL TITL BOOSTING AFFINITY BY CORRECT LIGAND PREORGANIZATION FOR THE JRNL TITL 2 S2 POCKET OF THROMBIN: A STUDY BY ISOTHERMAL TITRATION JRNL TITL 3 CALORIMETRY, MOLECULAR DYNAMICS, AND HIGH-RESOLUTION CRYSTAL JRNL TITL 4 STRUCTURES. JRNL REF CHEMMEDCHEM V. 11 309 2016 JRNL REFN ISSN 1860-7179 JRNL PMID 26762840 JRNL DOI 10.1002/CMDC.201500531 REMARK 2 REMARK 2 RESOLUTION. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 62347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3157 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 49.6904 - 4.0625 0.96 2627 139 0.1478 0.1699 REMARK 3 2 4.0625 - 3.2247 1.00 2708 134 0.1308 0.1503 REMARK 3 3 3.2247 - 2.8171 1.00 2695 124 0.1581 0.1712 REMARK 3 4 2.8171 - 2.5596 1.00 2662 157 0.1577 0.1732 REMARK 3 5 2.5596 - 2.3761 1.00 2669 132 0.1439 0.1600 REMARK 3 6 2.3761 - 2.2360 1.00 2686 140 0.1401 0.1675 REMARK 3 7 2.2360 - 2.1240 1.00 2649 131 0.1285 0.1526 REMARK 3 8 2.1240 - 2.0316 1.00 2670 139 0.1252 0.1470 REMARK 3 9 2.0316 - 1.9534 0.99 2645 135 0.1264 0.1445 REMARK 3 10 1.9534 - 1.8860 0.99 2633 127 0.1155 0.1667 REMARK 3 11 1.8860 - 1.8270 0.98 2633 152 0.1163 0.1379 REMARK 3 12 1.8270 - 1.7748 0.98 2595 155 0.1153 0.1516 REMARK 3 13 1.7748 - 1.7280 0.98 2580 147 0.1111 0.1428 REMARK 3 14 1.7280 - 1.6859 0.97 2609 111 0.1086 0.1443 REMARK 3 15 1.6859 - 1.6475 0.97 2572 142 0.1048 0.1267 REMARK 3 16 1.6475 - 1.6125 0.96 2532 134 0.1030 0.1286 REMARK 3 17 1.6125 - 1.5802 0.96 2582 145 0.1116 0.1620 REMARK 3 18 1.5802 - 1.5504 0.94 2496 131 0.1151 0.1421 REMARK 3 19 1.5504 - 1.5227 0.94 2464 148 0.1145 0.1861 REMARK 3 20 1.5227 - 1.4969 0.92 2449 138 0.1273 0.1876 REMARK 3 21 1.4969 - 1.4728 0.92 2399 135 0.1353 0.1801 REMARK 3 22 1.4728 - 1.4501 0.89 2390 139 0.1442 0.1712 REMARK 3 23 1.4501 - 1.4288 0.86 2245 122 0.1522 0.1863 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.90 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 2550 REMARK 3 ANGLE : 1.125 3469 REMARK 3 CHIRALITY : 0.074 361 REMARK 3 PLANARITY : 0.005 437 REMARK 3 DIHEDRAL : 17.496 1004 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 4UFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063350. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-09 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 49.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 (%): 50.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 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 35.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.00000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.80000 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: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.9 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 H2095 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 148 REMARK 465 THR H 149 REMARK 465 ALA H 149A REMARK 465 ASN H 149B REMARK 465 VAL H 149C REMARK 465 GLY H 149D REMARK 465 LYS H 149E REMARK 465 GLY I 554 REMARK 465 ASP I 555 REMARK 465 PHE I 556 REMARK 465 GLU I 557 REMARK 465 GLU I 558 REMARK 465 ILE I 559 REMARK 465 PRO I 560 REMARK 465 GLU I 561 REMARK 465 GLU L 0 REMARK 465 ASP L 15 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 CG CD CE NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 CG CD CE NZ REMARK 470 GLU I 562 N CA C O REMARK 470 GLN I 565 CG CD OE1 NE2 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 82.57 -152.71 REMARK 500 ASN H 60G 82.66 -157.18 REMARK 500 HIS H 71 -62.24 -130.57 REMARK 500 ILE H 79 -60.73 -126.63 REMARK 500 GLU H 97A -71.52 -117.95 REMARK 500 SER H 195 131.09 -33.94 REMARK 500 PHE L 7 -89.08 -129.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H2043 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH H2049 DISTANCE = 6.30 ANGSTROMS 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 LYS H 169 O REMARK 620 2 THR H 172 O 84.9 REMARK 620 3 PHE H 204A O 98.6 97.7 REMARK 620 4 HOH H2203 O 71.9 77.0 169.4 REMARK 620 5 HOH H2204 O 85.3 170.1 82.4 101.2 REMARK 620 6 HOH H2209 O 175.4 94.8 86.0 103.5 95.1 REMARK 620 N 1 2 3 4 5 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 ARG H 221A O REMARK 620 2 LYS H 224 O 93.4 REMARK 620 3 HOH H2225 O 161.4 70.5 REMARK 620 4 HOH H2226 O 89.1 93.3 82.6 REMARK 620 5 HOH H2236 O 97.3 83.1 90.3 172.7 REMARK 620 6 HOH H2257 O 106.2 160.3 89.9 85.5 95.8 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: (2S)-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]-1-[(2R)-3- REMARK 630 PHENYL-2-[(PHENYLMETHYL)SULFONYLAMINO]PROPANOYL]PYRROLIDINE-2- REMARK 630 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 S49 H 1251 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS PRO DPN 00S REMARK 630 DETAILS: NULL 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: 4UFE RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -(2-((4- REMARK 900 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-BUTYL)-3 -PHENYL-PROPANAMIDE REMARK 900 RELATED ID: 4UFF RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -(2-((4- REMARK 900 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-ETHYL)-N -METHYL-3-PHENYL- REMARK 900 PROPANAMIDE REMARK 900 RELATED ID: 4UFG RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -((1S)-2- REMARK 900 ((4-CARBAMIMIDOYLPHENYL)METHYLAMINO)-1-METHYL- 2-OXO-ETHYL)-N- REMARK 900 METHYL-3-PHENYL-PROPANAMIDE ETHANE REMARK 999 REMARK 999 SEQUENCE REMARK 999 GLU 1C AND ASP 14L WERE NOT BUILD DUE TO LACK OF ELECTRON REMARK 999 DENSITY REMARK 999 RESIDUES 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON REMARK 999 DENSITY REMARK 999 RESIDUE G554 WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY DBREF 4UFD H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 4UFD I 554 565 UNP P09945 HIRV2_HIRME 61 72 DBREF 4UFD L 1A 14K UNP P00734 THRB_HUMAN 333 361 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 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN SEQRES 1 L 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 L 29 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 L 29 TYR ILE ASP MODRES 4UFD ASN H 60G ASN GLYCOSYLATION SITE MODRES 4UFD TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NAG H1060 14 HET NA H1247 1 HET NA H1248 1 HET GOL H1249 6 HET GOL H1250 6 HET S49 H1251 39 HET PO4 H1252 5 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM S49 (2S)-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]-1-[(2R)-3- HETNAM 2 S49 PHENYL-2-[(PHENYLMETHYL) HETNAM 3 S49 SULFONYLAMINO]PROPANOYL]PYRROLIDINE-2-CARBOXAMIDE HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TYS C9 H11 N O6 S FORMUL 4 NAG C8 H15 N O6 FORMUL 5 NA 2(NA 1+) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 S49 C29 H33 N5 O4 S FORMUL 10 PO4 O4 P 3- FORMUL 11 HOH *307(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 LEU H 234 GLY H 246 1 13 HELIX 7 7 PHE L 7 SER L 11 5 5 HELIX 8 8 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 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H1060 1555 1555 1.42 LINK C TYS I 563 N LEU I 564 1555 1555 1.33 LINK O LYS H 169 NA NA H1247 1555 1555 2.34 LINK O THR H 172 NA NA H1247 1555 1555 2.32 LINK O PHE H 204A NA NA H1247 4546 1555 2.38 LINK O ARG H 221A NA NA H1248 1555 1555 2.34 LINK O LYS H 224 NA NA H1248 1555 1555 2.44 LINK NA NA H1247 O HOH H2203 1555 1555 2.61 LINK NA NA H1247 O HOH H2204 1555 1555 2.42 LINK NA NA H1247 O HOH H2209 1555 1555 2.37 LINK NA NA H1248 O HOH H2225 1555 1555 2.47 LINK NA NA H1248 O HOH H2226 1555 1555 2.61 LINK NA NA H1248 O HOH H2236 1555 1555 2.35 LINK NA NA H1248 O HOH H2257 1555 1555 2.35 CISPEP 1 SER H 36A PRO H 37 0 -3.93 CRYST1 70.000 71.600 71.900 90.00 100.00 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 0.014286 0.000000 0.002519 0.00000 SCALE2 0.000000 0.013966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014123 0.00000 MASTER 367 0 8 8 16 0 0 6 0 0 0 24 END