PDB Short entry for 4UFG HEADER HYDROLASE 17-MAR-15 4UFG TITLE THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N-((1S)-2-((4- TITLE 2 CARBAMIMIDOYLPHENYL)METHYLAMINO)-1-METHYL-2-OXO-ETHYL)-N-METHYL-3- TITLE 3 PHENYL-PROPANAMIDE ETHANE 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 4UFG 1 HETSYN REVDAT 3 29-JUL-20 4UFG 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 02-MAR-16 4UFG 1 JRNL REVDAT 1 27-JAN-16 4UFG 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 41818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2123 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 35.6902 - 4.0667 0.98 2677 152 0.1459 0.1515 REMARK 3 2 4.0667 - 3.2285 0.99 2696 146 0.1495 0.1707 REMARK 3 3 3.2285 - 2.8206 0.99 2660 128 0.1811 0.2067 REMARK 3 4 2.8206 - 2.5628 0.99 2676 148 0.1836 0.2057 REMARK 3 5 2.5628 - 2.3792 0.99 2647 117 0.1671 0.1921 REMARK 3 6 2.3792 - 2.2389 0.99 2696 138 0.1613 0.2058 REMARK 3 7 2.2389 - 2.1268 0.99 2617 168 0.1525 0.1794 REMARK 3 8 2.1268 - 2.0342 0.99 2629 154 0.1567 0.1849 REMARK 3 9 2.0342 - 1.9559 0.99 2661 124 0.1591 0.1849 REMARK 3 10 1.9559 - 1.8884 0.99 2659 151 0.1686 0.2082 REMARK 3 11 1.8884 - 1.8294 0.99 2591 158 0.1631 0.2143 REMARK 3 12 1.8294 - 1.7771 0.99 2651 130 0.1598 0.1785 REMARK 3 13 1.7771 - 1.7303 0.99 2626 132 0.1594 0.2105 REMARK 3 14 1.7303 - 1.6881 0.99 2657 121 0.1787 0.1973 REMARK 3 15 1.6881 - 1.6497 0.96 2552 156 0.1941 0.2245 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.96 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 : 0.006 2506 REMARK 3 ANGLE : 1.090 3402 REMARK 3 CHIRALITY : 0.047 356 REMARK 3 PLANARITY : 0.005 461 REMARK 3 DIHEDRAL : 15.352 988 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1C THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 131.9349 16.2421 89.5835 REMARK 3 T TENSOR REMARK 3 T11: 0.1529 T22: 0.0701 REMARK 3 T33: 0.0947 T12: 0.0411 REMARK 3 T13: 0.0296 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 3.8375 L22: 4.4563 REMARK 3 L33: 5.6887 L12: -0.7979 REMARK 3 L13: 2.2646 L23: 0.3665 REMARK 3 S TENSOR REMARK 3 S11: -0.0203 S12: 0.1704 S13: 0.2639 REMARK 3 S21: -0.0828 S22: -0.0735 S23: -0.1915 REMARK 3 S31: -0.4781 S32: 0.0304 S33: 0.0947 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 8 THROUGH 14B ) REMARK 3 ORIGIN FOR THE GROUP (A): 123.3400 14.2014 91.6323 REMARK 3 T TENSOR REMARK 3 T11: 0.1008 T22: 0.1244 REMARK 3 T33: 0.0971 T12: 0.0565 REMARK 3 T13: 0.0097 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 1.3793 L22: 9.4299 REMARK 3 L33: 3.7168 L12: -1.4725 REMARK 3 L13: 1.2996 L23: -3.2289 REMARK 3 S TENSOR REMARK 3 S11: 0.0583 S12: -0.0048 S13: 0.0829 REMARK 3 S21: -0.0071 S22: -0.0643 S23: 0.2214 REMARK 3 S31: -0.1982 S32: -0.2149 S33: 0.0099 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14K ) REMARK 3 ORIGIN FOR THE GROUP (A): 125.6979 7.2980 103.9136 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.1363 REMARK 3 T33: 0.1304 T12: 0.0399 REMARK 3 T13: 0.0490 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 4.8137 L22: 5.0486 REMARK 3 L33: 1.9994 L12: 0.8095 REMARK 3 L13: 0.1001 L23: -1.9322 REMARK 3 S TENSOR REMARK 3 S11: -0.0589 S12: -0.4138 S13: -0.0468 REMARK 3 S21: 0.1901 S22: 0.0959 S23: 0.1377 REMARK 3 S31: -0.0253 S32: -0.3014 S33: -0.0045 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 60I ) REMARK 3 ORIGIN FOR THE GROUP (A): 142.0194 -1.5067 84.1645 REMARK 3 T TENSOR REMARK 3 T11: 0.1307 T22: 0.1580 REMARK 3 T33: 0.0993 T12: 0.0534 REMARK 3 T13: -0.0070 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 1.1108 L22: 1.3654 REMARK 3 L33: 1.0704 L12: -0.7870 REMARK 3 L13: 0.4680 L23: -0.1859 REMARK 3 S TENSOR REMARK 3 S11: 0.2472 S12: 0.3941 S13: -0.0972 REMARK 3 S21: -0.2038 S22: -0.2150 S23: -0.0363 REMARK 3 S31: 0.1380 S32: 0.1170 S33: -0.0096 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 61 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 135.9549 1.9300 74.8683 REMARK 3 T TENSOR REMARK 3 T11: 0.2373 T22: 0.3059 REMARK 3 T33: 0.1111 T12: 0.1043 REMARK 3 T13: -0.0168 T23: -0.0486 REMARK 3 L TENSOR REMARK 3 L11: 0.6197 L22: 1.4387 REMARK 3 L33: 0.3408 L12: -0.0631 REMARK 3 L13: -0.4162 L23: -0.2474 REMARK 3 S TENSOR REMARK 3 S11: 0.2020 S12: 0.4997 S13: -0.1688 REMARK 3 S21: -0.4075 S22: -0.1680 S23: 0.0305 REMARK 3 S31: 0.2483 S32: 0.1560 S33: -0.0398 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 81 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 145.0619 4.7674 91.5923 REMARK 3 T TENSOR REMARK 3 T11: 0.0951 T22: 0.1081 REMARK 3 T33: 0.1085 T12: 0.0060 REMARK 3 T13: 0.0002 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.8954 L22: 0.9870 REMARK 3 L33: 0.8723 L12: -0.9295 REMARK 3 L13: 0.0751 L23: 0.3167 REMARK 3 S TENSOR REMARK 3 S11: 0.0714 S12: 0.0897 S13: 0.1449 REMARK 3 S21: 0.0042 S22: -0.0448 S23: -0.1484 REMARK 3 S31: -0.0150 S32: 0.1611 S33: -0.0277 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 141 THROUGH 197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 135.8741 -7.4030 98.4438 REMARK 3 T TENSOR REMARK 3 T11: 0.1278 T22: 0.0808 REMARK 3 T33: 0.1367 T12: -0.0013 REMARK 3 T13: 0.0019 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.3058 L22: 1.5858 REMARK 3 L33: 1.4997 L12: -0.8864 REMARK 3 L13: 0.4898 L23: -0.7639 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: -0.0472 S13: -0.2365 REMARK 3 S21: 0.0303 S22: 0.0492 S23: 0.1847 REMARK 3 S31: 0.2093 S32: -0.0627 S33: -0.0530 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 198 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 137.3189 0.4873 98.7268 REMARK 3 T TENSOR REMARK 3 T11: 0.0820 T22: 0.0819 REMARK 3 T33: 0.0757 T12: 0.0173 REMARK 3 T13: 0.0036 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.7640 L22: 1.0847 REMARK 3 L33: 1.2562 L12: -0.3574 REMARK 3 L13: 0.0489 L23: 0.1868 REMARK 3 S TENSOR REMARK 3 S11: 0.0405 S12: -0.0657 S13: -0.1336 REMARK 3 S21: 0.0422 S22: -0.0139 S23: 0.0475 REMARK 3 S31: 0.0695 S32: -0.0012 S33: -0.0284 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 232 THROUGH 247 ) REMARK 3 ORIGIN FOR THE GROUP (A): 153.5136 10.3387 93.9289 REMARK 3 T TENSOR REMARK 3 T11: 0.1470 T22: 0.1532 REMARK 3 T33: 0.2608 T12: -0.0243 REMARK 3 T13: 0.0152 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 5.9057 L22: 4.6123 REMARK 3 L33: 3.8039 L12: 1.2083 REMARK 3 L13: -3.8700 L23: -1.9863 REMARK 3 S TENSOR REMARK 3 S11: 0.2068 S12: 0.0537 S13: 0.6426 REMARK 3 S21: -0.0786 S22: -0.0456 S23: -0.3598 REMARK 3 S31: -0.4779 S32: 0.5037 S33: -0.1781 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 555 THROUGH 565 ) REMARK 3 ORIGIN FOR THE GROUP (A): 138.9560 0.6128 68.1226 REMARK 3 T TENSOR REMARK 3 T11: 0.4040 T22: 0.6023 REMARK 3 T33: 0.2115 T12: 0.1334 REMARK 3 T13: 0.0663 T23: -0.0843 REMARK 3 L TENSOR REMARK 3 L11: 0.5321 L22: 2.2135 REMARK 3 L33: 0.8464 L12: -0.4393 REMARK 3 L13: -0.3487 L23: 0.5763 REMARK 3 S TENSOR REMARK 3 S11: 0.1261 S12: 0.4588 S13: -0.0328 REMARK 3 S21: -0.7220 S22: 0.0644 S23: -0.3294 REMARK 3 S31: -0.0755 S32: 0.1430 S33: -0.0428 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 4UFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063355. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41835 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 35.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 18.80 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 4UE7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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 35.04600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.62450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.04600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.62450 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.6 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 H2062 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 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 CG CD NE CZ NH1 NH2 REMARK 470 LYS H 60F CG CD CE NZ REMARK 470 LYS H 107 CE NZ REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 LYS H 145 CE NZ REMARK 470 LYS H 169 NZ REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 LYS H 240 CE NZ 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 470 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 14A CE NZ REMARK 470 ASP L 15 CA C O CB CG OD1 OD2 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 86.32 -152.59 REMARK 500 ASN H 60G 78.88 -157.69 REMARK 500 HIS H 71 -60.85 -127.76 REMARK 500 ILE H 79 -59.37 -127.62 REMARK 500 SER H 214 -59.45 -123.11 REMARK 500 PHE L 7 -87.29 -128.93 REMARK 500 ILE L 14K -110.95 -92.92 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 H2041 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH L2026 DISTANCE = 6.85 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 H1247 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 80.9 REMARK 620 3 HOH H2142 O 69.3 73.3 REMARK 620 N 1 2 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 94.1 REMARK 620 3 HOH H2159 O 163.5 71.1 REMARK 620 4 HOH H2161 O 91.7 94.0 82.3 REMARK 620 5 HOH H2171 O 96.1 82.9 89.5 171.8 REMARK 620 6 HOH H2190 O 107.1 158.8 87.8 84.7 95.4 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: 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 999 REMARK 999 SEQUENCE 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 4UFG H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 4UFG I 554 565 UNP P09945 HIRV2_HIRME 61 72 DBREF 4UFG 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 4UFG ASN H 60G ASN GLYCOSYLATION SITE MODRES 4UFG TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NA H1247 1 HET NA H1248 1 HET D6J H1249 39 HET PO4 H1250 5 HET NAG H1251 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM D6J (2S)-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]-2-[METHYL-[(2R)- HETNAM 2 D6J 3-PHENYL-2-[(PHENYLMETHYL) HETNAM 3 D6J SULFONYLAMINO]PROPANOYL]AMINO]BUTANAMIDE 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 D6J C29 H35 N5 O4 S FORMUL 7 PO4 O4 P 3- FORMUL 8 NAG C8 H15 N O6 FORMUL 9 HOH *234(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 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 2.04 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H1251 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 H1247 1555 1555 2.40 LINK O THR H 172 NA NA H1247 1555 1555 2.38 LINK O ARG H 221A NA NA H1248 1555 1555 2.37 LINK O LYS H 224 NA NA H1248 1555 1555 2.42 LINK NA NA H1247 O HOH H2142 1555 1555 2.85 LINK NA NA H1248 O HOH H2159 1555 1555 2.44 LINK NA NA H1248 O HOH H2161 1555 1555 2.60 LINK NA NA H1248 O HOH H2171 1555 1555 2.33 LINK NA NA H1248 O HOH H2190 1555 1555 2.40 CISPEP 1 SER H 36A PRO H 37 0 -1.97 CRYST1 70.092 71.249 72.587 90.00 100.53 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 0.014267 0.000000 0.002652 0.00000 SCALE2 0.000000 0.014035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014013 0.00000