HEADER HYDROLASE 16-MAR-15 4UFF TITLE THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N-(2-((4- TITLE 2 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-ETHYL)-N-METHYL-3-PHENYL- TITLE 3 PROPANAMIDE 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 4 20-DEC-23 4UFF 1 HETSYN REVDAT 3 29-JUL-20 4UFF 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 02-MAR-16 4UFF 1 JRNL REVDAT 1 27-JAN-16 4UFF 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 50764 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2538 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 35.6293 - 4.0600 0.95 2640 139 0.1395 0.1751 REMARK 3 2 4.0600 - 3.2233 0.99 2703 142 0.1435 0.1514 REMARK 3 3 3.2233 - 2.8160 0.99 2674 141 0.1701 0.1984 REMARK 3 4 2.8160 - 2.5586 0.99 2696 142 0.1730 0.2031 REMARK 3 5 2.5586 - 2.3753 0.99 2681 141 0.1601 0.1744 REMARK 3 6 2.3753 - 2.2352 0.99 2690 142 0.1546 0.1900 REMARK 3 7 2.2352 - 2.1233 0.99 2669 140 0.1484 0.1857 REMARK 3 8 2.1233 - 2.0309 0.99 2696 142 0.1522 0.1930 REMARK 3 9 2.0309 - 1.9527 0.99 2670 141 0.1530 0.1677 REMARK 3 10 1.9527 - 1.8853 0.99 2681 141 0.1585 0.2080 REMARK 3 11 1.8853 - 1.8264 1.00 2694 141 0.1615 0.1940 REMARK 3 12 1.8264 - 1.7742 1.00 2691 142 0.1610 0.1735 REMARK 3 13 1.7742 - 1.7275 0.99 2650 140 0.1775 0.2028 REMARK 3 14 1.7275 - 1.6853 0.99 2684 141 0.1861 0.2281 REMARK 3 15 1.6853 - 1.6470 0.99 2709 142 0.2013 0.2341 REMARK 3 16 1.6470 - 1.6120 0.99 2640 139 0.2064 0.2757 REMARK 3 17 1.6120 - 1.5797 0.99 2706 143 0.2253 0.2265 REMARK 3 18 1.5797 - 1.5499 0.99 2652 139 0.2275 0.2539 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90 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 : 0.006 2502 REMARK 3 ANGLE : 1.083 3392 REMARK 3 CHIRALITY : 0.045 354 REMARK 3 PLANARITY : 0.005 457 REMARK 3 DIHEDRAL : 14.872 992 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1B THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.4138 21.8692 160.6716 REMARK 3 T TENSOR REMARK 3 T11: 0.1947 T22: 0.0969 REMARK 3 T33: 0.1430 T12: 0.0440 REMARK 3 T13: 0.0195 T23: 0.0209 REMARK 3 L TENSOR REMARK 3 L11: 5.2700 L22: 1.4385 REMARK 3 L33: 6.1645 L12: -1.9577 REMARK 3 L13: 2.9535 L23: 0.4238 REMARK 3 S TENSOR REMARK 3 S11: -0.1003 S12: 0.2660 S13: 0.4171 REMARK 3 S21: -0.2193 S22: -0.0916 S23: -0.0832 REMARK 3 S31: -0.4635 S32: 0.0396 S33: 0.1767 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 8 THROUGH 14B ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.3661 19.8482 162.7607 REMARK 3 T TENSOR REMARK 3 T11: 0.1199 T22: 0.1698 REMARK 3 T33: 0.1501 T12: 0.0676 REMARK 3 T13: -0.0004 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 1.6301 L22: 7.9135 REMARK 3 L33: 4.4070 L12: -1.3467 REMARK 3 L13: 0.3424 L23: -3.5787 REMARK 3 S TENSOR REMARK 3 S11: 0.0428 S12: -0.0440 S13: 0.0510 REMARK 3 S21: 0.0703 S22: 0.0408 S23: 0.3666 REMARK 3 S31: -0.2343 S32: -0.3724 S33: -0.0474 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14K ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.8270 13.1100 174.9011 REMARK 3 T TENSOR REMARK 3 T11: 0.1253 T22: 0.1506 REMARK 3 T33: 0.1653 T12: 0.0386 REMARK 3 T13: 0.0627 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 5.3367 L22: 5.0243 REMARK 3 L33: 7.5410 L12: 1.1087 REMARK 3 L13: 0.5667 L23: -0.3065 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: -0.5417 S13: -0.0365 REMARK 3 S21: 0.3630 S22: 0.0380 S23: 0.2669 REMARK 3 S31: -0.1292 S32: -0.3879 S33: -0.0049 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.5403 5.2392 152.4579 REMARK 3 T TENSOR REMARK 3 T11: 0.1836 T22: 0.2072 REMARK 3 T33: 0.1200 T12: 0.0847 REMARK 3 T13: -0.0100 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 1.0636 L22: 1.4678 REMARK 3 L33: 1.0439 L12: -0.6641 REMARK 3 L13: 0.3526 L23: -0.1295 REMARK 3 S TENSOR REMARK 3 S11: 0.2848 S12: 0.4441 S13: -0.1460 REMARK 3 S21: -0.3292 S22: -0.2460 S23: -0.0052 REMARK 3 S31: 0.1723 S32: 0.1105 S33: -0.0207 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 81 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.8819 7.9174 162.5623 REMARK 3 T TENSOR REMARK 3 T11: 0.1020 T22: 0.0965 REMARK 3 T33: 0.0866 T12: 0.0205 REMARK 3 T13: -0.0089 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.9556 L22: 1.4415 REMARK 3 L33: 1.1687 L12: -0.9176 REMARK 3 L13: -0.0015 L23: -0.0720 REMARK 3 S TENSOR REMARK 3 S11: 0.0855 S12: 0.0710 S13: -0.0031 REMARK 3 S21: -0.0542 S22: -0.0635 S23: -0.0530 REMARK 3 S31: 0.0578 S32: 0.1175 S33: -0.0184 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 165 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 62.7196 -3.2558 178.2118 REMARK 3 T TENSOR REMARK 3 T11: 0.2286 T22: 0.1864 REMARK 3 T33: 0.1708 T12: 0.0466 REMARK 3 T13: -0.0115 T23: 0.0376 REMARK 3 L TENSOR REMARK 3 L11: 0.3590 L22: 1.9866 REMARK 3 L33: 0.8109 L12: 0.3159 REMARK 3 L13: -0.5334 L23: -0.2468 REMARK 3 S TENSOR REMARK 3 S11: -0.0969 S12: -0.1809 S13: -0.0827 REMARK 3 S21: 0.4160 S22: 0.0778 S23: -0.1125 REMARK 3 S31: 0.0753 S32: 0.0717 S33: 0.0148 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 180 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.2429 3.5481 170.0299 REMARK 3 T TENSOR REMARK 3 T11: 0.1080 T22: 0.0893 REMARK 3 T33: 0.1238 T12: 0.0130 REMARK 3 T13: 0.0121 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.7032 L22: 2.1517 REMARK 3 L33: 1.4870 L12: -0.3859 REMARK 3 L13: 0.2090 L23: 0.0272 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: -0.1277 S13: -0.2695 REMARK 3 S21: 0.1361 S22: 0.0370 S23: 0.1665 REMARK 3 S31: 0.1787 S32: -0.0301 S33: -0.0370 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 232 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.4839 15.9789 165.4056 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.2175 REMARK 3 T33: 0.3402 T12: -0.0257 REMARK 3 T13: 0.0205 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 6.5656 L22: 5.2990 REMARK 3 L33: 2.7941 L12: 1.5386 REMARK 3 L13: -4.1133 L23: -1.7874 REMARK 3 S TENSOR REMARK 3 S11: 0.2777 S12: 0.0289 S13: 0.6998 REMARK 3 S21: -0.0030 S22: -0.0565 S23: -0.5691 REMARK 3 S31: -0.5584 S32: 0.4894 S33: -0.2274 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 555 THROUGH 564 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.4495 6.3536 139.3905 REMARK 3 T TENSOR REMARK 3 T11: 0.4692 T22: 0.6183 REMARK 3 T33: 0.1812 T12: 0.2149 REMARK 3 T13: 0.0485 T23: -0.0799 REMARK 3 L TENSOR REMARK 3 L11: 0.0781 L22: 1.0924 REMARK 3 L33: 1.8336 L12: -0.2729 REMARK 3 L13: -0.2858 L23: 1.3269 REMARK 3 S TENSOR REMARK 3 S11: 0.0727 S12: 0.2774 S13: -0.0130 REMARK 3 S21: -0.4317 S22: 0.0679 S23: -0.1557 REMARK 3 S31: -0.1186 S32: 0.0995 S33: 0.1495 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 4UFF 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_1290063353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-14 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 : BESSY REMARK 200 BEAMLINE : 14.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.896 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 35.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.340 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: 1H8D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.71 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 35.21450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.78100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.21450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.78100 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 H2067 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 GLU L 1C 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 ARG H 50 CD NE CZ NH1 NH2 REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 LYS H 145 NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 GLN H 151 CG CD OE1 NE2 REMARK 470 ASP H 186A OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 LYS H 240 CG CD CE NZ REMARK 470 GLN H 244 OE1 NE2 REMARK 470 GLY H 246 CA C O REMARK 470 ASP I 555 CG 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 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 83.86 -154.93 REMARK 500 ASN H 60G 82.43 -158.16 REMARK 500 HIS H 71 -63.13 -131.38 REMARK 500 ILE H 79 -61.29 -126.63 REMARK 500 GLU H 97A -67.58 -109.81 REMARK 500 PHE L 7 -89.06 -130.35 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 H2046 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH H2196 DISTANCE = 5.85 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 H1246 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 81.0 REMARK 620 3 HOH H2145 O 85.3 166.3 REMARK 620 4 HOH H2146 O 71.2 74.4 101.7 REMARK 620 5 HOH H2150 O 173.9 94.4 99.2 103.8 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 93.7 REMARK 620 3 HOH H2162 O 160.8 68.8 REMARK 620 4 HOH H2163 O 90.8 93.0 82.5 REMARK 620 5 HOH H2171 O 97.8 82.9 88.2 170.7 REMARK 620 6 HOH H2184 O 108.3 157.9 89.1 84.8 95.8 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: 4UFD RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 4-(((1-((2S)-1-((2R)-2-( REMARK 900 BENZYLSULFONYLAMINO)-3-PHENYL-PROPANOYL)PYRROLIDIN-2-YL)- 1-OXO- REMARK 900 ETHYL)AMINO)METHYL)BENZAMIDINE 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: 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 DBREF 4UFF H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 4UFF I 554 565 UNP P09945 HIRV2_HIRME 61 72 DBREF 4UFF L 1C 15 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 4UFF ASN H 60G ASN GLYCOSYLATION SITE MODRES 4UFF TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NA H1246 1 HET NA H1247 1 HET 6V2 H1248 37 HET PO4 H1249 5 HET NAG H1260 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM 6V2 (2R)-2-(BENZYLSULFONYLAMINO)-N-(2-((4- HETNAM 2 6V2 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-ETHYL)-N- HETNAM 3 6V2 METHYL-3-PHENYL-PROPANAMIDE HETNAM PO4 PHOSPHATE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 6V2 C27 H31 N5 O4 S FORMUL 7 PO4 O4 P 3- FORMUL 8 NAG C8 H15 N O6 FORMUL 9 HOH *223(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 PHE H 245 1 12 HELIX 8 8 PRO I 560 LEU I 564 5 5 HELIX 9 9 PHE L 7 SER L 11 5 5 HELIX 10 10 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 2.03 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 LINK ND2 ASN H 60G C1 NAG H1260 1555 1555 1.43 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 H1246 1555 1555 2.40 LINK O THR H 172 NA NA H1246 1555 1555 2.37 LINK O ARG H 221A NA NA H1247 1555 1555 2.30 LINK O LYS H 224 NA NA H1247 1555 1555 2.46 LINK NA NA H1246 O HOH H2145 1555 1555 2.47 LINK NA NA H1246 O HOH H2146 1555 1555 2.68 LINK NA NA H1246 O HOH H2150 1555 1555 2.33 LINK NA NA H1247 O HOH H2162 1555 1555 2.48 LINK NA NA H1247 O HOH H2163 1555 1555 2.61 LINK NA NA H1247 O HOH H2171 1555 1555 2.29 LINK NA NA H1247 O HOH H2184 1555 1555 2.38 CISPEP 1 SER H 36A PRO H 37 0 -2.71 CRYST1 70.429 71.562 72.450 90.00 100.49 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 0.014199 0.000000 0.002629 0.00000 SCALE2 0.000000 0.013974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014037 0.00000