HEADER BLOOD CLOTTING 08-DEC-16 5MM6 TITLE THROMBIN MUTANT A190S IN COMPLEX WITH (S)-1-(D-PHENYLALANYL)-N-(4- TITLE 2 CARBAMIMIDOYLBENZYL)PYRROLIDINE-2-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 SYNONYM: COAGULATION FACTOR II; COMPND 11 EC: 3.4.21.5; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: ALANINE 190 MUTATED TO SERINE; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: HIRUDIN VARIANT-2; COMPND 16 CHAIN: I; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: HTTP://SHOP.BACHEM.COM/H-7525.HTML CONTAINS SULFATED COMPND 19 TYROSINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 GENE: F2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PT2 A190S; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 TISSUE: BLOOD; SOURCE 17 GENE: F2; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PT2 A190S; SOURCE 23 MOL_ID: 3; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 26 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 27 ORGANISM_TAXID: 6421 KEYWDS COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 2 BLOOD CLOTTING INHIBITOR; PREORGANIZATION; GLYCOSILATION; BLOOD; KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MARCA,A.SANDNER,A.HEINE,G.KLEBE REVDAT 2 27-JUN-18 5MM6 1 REMARK REVDAT 1 20-DEC-17 5MM6 0 JRNL AUTH A.MARCA,A.SANDNER,A.HEINE,G.KLEBE JRNL TITL THROMBIN MUTANT A190S IN COMPLEX WITH JRNL TITL 2 (S)-1-(D-PHENYLALANYL)-N-(4-CARBAMIMIDOYLBENZYL) JRNL TITL 3 PYRROLIDINE-2-CARBOXAMIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 85676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4285 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 43.6018 - 4.0082 0.97 2807 148 0.1450 0.1494 REMARK 3 2 4.0082 - 3.1817 0.97 2747 145 0.1269 0.1363 REMARK 3 3 3.1817 - 2.7796 0.98 2780 146 0.1365 0.1424 REMARK 3 4 2.7796 - 2.5255 0.99 2787 147 0.1262 0.1394 REMARK 3 5 2.5255 - 2.3445 0.97 2749 145 0.1151 0.1324 REMARK 3 6 2.3445 - 2.2063 0.94 2660 140 0.1217 0.1453 REMARK 3 7 2.2063 - 2.0958 0.98 2755 145 0.0981 0.1309 REMARK 3 8 2.0958 - 2.0045 0.98 2751 144 0.0974 0.1156 REMARK 3 9 2.0045 - 1.9274 0.98 2733 144 0.0986 0.1201 REMARK 3 10 1.9274 - 1.8609 0.96 2708 143 0.1103 0.1331 REMARK 3 11 1.8609 - 1.8027 0.98 2777 146 0.0927 0.1158 REMARK 3 12 1.8027 - 1.7511 0.97 2739 144 0.0882 0.1197 REMARK 3 13 1.7511 - 1.7050 0.98 2753 145 0.0849 0.1186 REMARK 3 14 1.7050 - 1.6634 0.98 2726 143 0.0888 0.1193 REMARK 3 15 1.6634 - 1.6256 0.98 2745 145 0.0862 0.1261 REMARK 3 16 1.6256 - 1.5910 0.98 2745 144 0.0921 0.1159 REMARK 3 17 1.5910 - 1.5592 0.97 2737 144 0.0961 0.1164 REMARK 3 18 1.5592 - 1.5298 0.97 2695 142 0.0987 0.1252 REMARK 3 19 1.5298 - 1.5025 0.96 2738 144 0.1075 0.1567 REMARK 3 20 1.5025 - 1.4770 0.97 2659 140 0.1197 0.1541 REMARK 3 21 1.4770 - 1.4532 0.96 2737 144 0.1240 0.1575 REMARK 3 22 1.4532 - 1.4308 0.96 2659 140 0.1476 0.1841 REMARK 3 23 1.4308 - 1.4098 0.95 2684 142 0.1461 0.1833 REMARK 3 24 1.4098 - 1.3899 0.96 2691 141 0.1596 0.2016 REMARK 3 25 1.3899 - 1.3711 0.96 2709 143 0.1589 0.1851 REMARK 3 26 1.3711 - 1.3533 0.96 2651 139 0.1737 0.1986 REMARK 3 27 1.3533 - 1.3364 0.96 2713 143 0.1840 0.2373 REMARK 3 28 1.3364 - 1.3203 0.95 2659 140 0.2015 0.2281 REMARK 3 29 1.3203 - 1.3049 0.95 2661 140 0.2427 0.2880 REMARK 3 30 1.3049 - 1.2903 0.88 2436 129 0.3437 0.3437 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2495 REMARK 3 ANGLE : 1.067 3382 REMARK 3 CHIRALITY : 0.088 349 REMARK 3 PLANARITY : 0.007 448 REMARK 3 DIHEDRAL : 18.797 952 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 5MM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 43.577 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.360 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM DIHYDROGEN PHOSPHATE PH REMARK 280 7.5, 350 MM NACL, 27% PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 35.17200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.82450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.17200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.82450 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: 5330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 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 H 407 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 THR L -4 REMARK 465 PHE L -3 REMARK 465 GLY L -2 REMARK 465 SER L -1 REMARK 465 GLY L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 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 147F REMARK 465 LYS H 147G REMARK 465 GLU H 247 REMARK 465 GLY I 517 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 L 1C CG CD OE1 OE2 REMARK 470 LYS L 9 NZ REMARK 470 GLU L 13 CD OE1 OE2 REMARK 470 LYS L 14A NZ REMARK 470 ILE L 14K CG1 CG2 CD1 REMARK 470 GLU H 18 OE1 OE2 REMARK 470 SER H 36A OG REMARK 470 ARG H 50 CG CD NE CZ NH1 NH2 REMARK 470 GLU H 86 OE1 OE2 REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 107 NZ REMARK 470 LYS H 110 CD CE NZ REMARK 470 LYS H 145 CD CE NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 ASP H 186A OD1 OD2 REMARK 470 LYS H 186D CD CE NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 LYS H 240 CD CE NZ REMARK 470 GLN H 244 CG CD OE1 NE2 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 GLU I 525 CD OE1 OE2 REMARK 470 GLN I 528 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 PHE L 7 -90.09 -130.90 REMARK 500 CYS H 42 -171.30 174.76 REMARK 500 TYR H 60A 85.48 -153.72 REMARK 500 ASN H 60G 80.31 -154.27 REMARK 500 HIS H 71 -60.81 -127.82 REMARK 500 ILE H 79 -60.25 -128.88 REMARK 500 GLU H 97A -73.73 -117.65 REMARK 500 SER H 195 135.16 -38.67 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 309 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 83.6 REMARK 620 3 HOH H 470 O 66.7 74.6 REMARK 620 4 PHE H 204A O 15.3 87.7 53.5 REMARK 620 5 HOH H 469 O 173.6 93.7 107.0 159.3 REMARK 620 6 HOH H 569 O 88.8 171.2 98.4 83.8 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 308 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 92.7 REMARK 620 3 HOH H 461 O 105.7 161.6 REMARK 620 4 HOH H 501 O 88.8 94.6 86.9 REMARK 620 5 HOH H 564 O 96.6 81.4 95.3 173.4 REMARK 620 6 HOH H 476 O 161.6 72.1 90.0 82.4 91.4 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-{4-[AMINO(IMINIO)METHYL]BENZYL}-L- REMARK 630 PROLINAMIDE 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 32U H 311 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO 00S REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS H 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS H 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 H 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 32U H 311 DBREF 5MM6 L -4 17 UNP P00734 THRB_HUMAN 328 363 DBREF 5MM6 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 5MM6 I 517 528 UNP P09945 HIRV2_HIRME 61 72 SEQADV 5MM6 SER H 190 UNP P00734 ALA 563 ENGINEERED MUTATION 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 SER 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 MODRES 5MM6 TYS I 526 TYR MODIFIED RESIDUE HET TYS I 526 25 HET GOL H 301 6 HET GOL H 302 6 HET GOL H 303 6 HET DMS H 304 4 HET DMS H 305 4 HET PO4 H 306 5 HET GOL H 307 6 HET NA H 308 1 HET NA H 309 1 HET GOL H 310 6 HET 32U H 311 29 HETNAM TYS O-SULFO-L-TYROSINE HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETNAM 32U D-PHENYLALANYL-N-{4-[AMINO(IMINIO)METHYL]BENZYL}-L- HETNAM 2 32U PROLINAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 GOL 5(C3 H8 O3) FORMUL 7 DMS 2(C2 H6 O S) FORMUL 9 PO4 O4 P 3- FORMUL 11 NA 2(NA 1+) FORMUL 14 32U C22 H28 N5 O2 1+ FORMUL 15 HOH *224(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 GLY H 246 1 13 HELIX 10 AB1 PRO I 523 LEU I 527 5 5 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.05 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.05 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK O LYS H 169 NA NA H 309 1555 1555 2.34 LINK O THR H 172 NA NA H 309 1555 1555 2.31 LINK O ARG H 221A NA NA H 308 1555 1555 2.35 LINK O LYS H 224 NA NA H 308 1555 1555 2.40 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 NA NA H 308 O HOH H 461 1555 1555 2.37 LINK NA NA H 308 O HOH H 501 1555 1555 2.64 LINK NA NA H 308 O HOH H 564 1555 1555 2.31 LINK NA NA H 308 O HOH H 476 1555 1555 2.44 LINK NA NA H 309 O HOH H 470 1555 1555 2.94 LINK O PHE H 204A NA NA H 309 1555 4556 2.39 LINK NA NA H 309 O HOH H 469 1555 4546 2.38 LINK NA NA H 309 O HOH H 569 1555 4546 2.34 CISPEP 1 SER H 36A PRO H 37 0 -3.54 SITE 1 AC1 8 ARG H 93 ARG H 165 ILE H 176 THR H 177 SITE 2 AC1 8 ASP H 178 PO4 H 306 HOH H 467 HOH H 563 SITE 1 AC2 5 ARG H 93 ARG H 165 ASP H 178 HIS H 230 SITE 2 AC2 5 HOH H 413 SITE 1 AC3 4 ARG H 93 ASN H 95 PO4 H 306 HOH H 408 SITE 1 AC4 4 LEU H 130 ARG H 165 PHE H 181 HOH H 455 SITE 1 AC5 4 PHE H 204A GLY H 223 LYS H 224 HOH H 401 SITE 1 AC6 9 ASN H 95 ASP H 100 ARG H 101 ARG H 175 SITE 2 AC6 9 GOL H 301 GOL H 303 HOH H 402 HOH H 428 SITE 3 AC6 9 HOH H 583 SITE 1 AC7 4 ARG H 173 PHE H 204A HOH H 416 HOH H 590 SITE 1 AC8 6 ARG H 221A LYS H 224 HOH H 461 HOH H 476 SITE 2 AC8 6 HOH H 501 HOH H 564 SITE 1 AC9 6 LYS H 169 THR H 172 PHE H 204A HOH H 469 SITE 2 AC9 6 HOH H 470 HOH H 569 SITE 1 AD1 7 LEU H 41 CYS H 42 TRP H 60D GLU H 192 SITE 2 AD1 7 GLY H 193 SER H 195 32U H 311 SITE 1 AD2 18 HIS H 57 TYR H 60A GLU H 97A ASP H 189 SITE 2 AD2 18 SER H 190 GLU H 192 SER H 195 VAL H 213 SITE 3 AD2 18 SER H 214 TRP H 215 GLY H 216 GLY H 219 SITE 4 AD2 18 GLY H 226 GOL H 310 HOH H 462 HOH H 492 SITE 5 AD2 18 HOH H 533 HOH H 549 CRYST1 70.344 71.649 72.538 90.00 100.48 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 0.014216 0.000000 0.002630 0.00000 SCALE2 0.000000 0.013957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014020 0.00000