HEADER HYDROLASE/HYDROLASE INHIBITOR 20-APR-11 3RLY TITLE HUMAN THROMBIN IN COMPLEX WITH MI329 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIRUDIN VARIANT-2; COMPND 11 CHAIN: I; COMPND 12 FRAGMENT: RESIDUES IN UNP 60-72; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 12 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 13 ORGANISM_TAXID: 6421; SOURCE 14 OTHER_DETAILS: SYNTHETIC FRAGMENT OF HIRUDIN FROM HIRUDO MEDICINALIS KEYWDS SERINE PROTEASE, KRINGLE, HYDROLASE, BLOOD COAGULATION, BLOOD KEYWDS 2 CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, CLEAVAGE ON PAIRS OF KEYWDS 3 BASIC RESIDUES, HIRUDIN, GLYCOSYLATION, BLOOD, HYDROLASE-HYDROLASE KEYWDS 4 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.BIELA,A.HEINE,G.KLEBE REVDAT 5 06-DEC-23 3RLY 1 REMARK REVDAT 4 01-NOV-23 3RLY 1 HETSYN REVDAT 3 29-JUL-20 3RLY 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 13-JUL-16 3RLY 1 JRNL REVDAT 1 25-APR-12 3RLY 0 JRNL AUTH A.BIELA,F.SIELAFF,F.TERWESTEN,A.HEINE,T.STEINMETZER,G.KLEBE JRNL TITL LIGAND BINDING STEPWISE DISRUPTS WATER NETWORK IN THROMBIN: JRNL TITL 2 ENTHALPIC AND ENTROPIC CHANGES REVEAL CLASSICAL HYDROPHOBIC JRNL TITL 3 EFFECT JRNL REF J.MED.CHEM. V. 55 6094 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22612268 JRNL DOI 10.1021/JM300337Q REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 52718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2659 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 35.6265 - 3.2527 0.99 5330 265 0.1490 0.1493 REMARK 3 2 3.2527 - 2.5820 0.99 5244 271 0.1641 0.1766 REMARK 3 3 2.5820 - 2.2556 0.99 5190 273 0.1529 0.1830 REMARK 3 4 2.2556 - 2.0494 0.99 5253 250 0.1440 0.1753 REMARK 3 5 2.0494 - 1.9026 0.98 5113 249 0.1397 0.1644 REMARK 3 6 1.9026 - 1.7904 0.96 4942 299 0.1419 0.1605 REMARK 3 7 1.7904 - 1.7007 0.95 4968 282 0.1513 0.1647 REMARK 3 8 1.7007 - 1.6267 0.92 4806 262 0.1679 0.1869 REMARK 3 9 1.6267 - 1.5641 0.90 4674 252 0.1862 0.2309 REMARK 3 10 1.5641 - 1.5101 0.87 4539 256 0.2155 0.2405 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 49.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.32780 REMARK 3 B22 (A**2) : -2.00290 REMARK 3 B33 (A**2) : -0.32490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.27160 REMARK 3 B23 (A**2) : 0.00000 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 2616 REMARK 3 ANGLE : 1.114 3561 REMARK 3 CHIRALITY : 0.075 368 REMARK 3 PLANARITY : 0.005 452 REMARK 3 DIHEDRAL : 17.741 1048 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 16:37) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7273 -2.0849 12.2417 REMARK 3 T TENSOR REMARK 3 T11: 0.1271 T22: 0.1392 REMARK 3 T33: 0.1082 T12: 0.0460 REMARK 3 T13: -0.0259 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 1.2734 L22: 0.7913 REMARK 3 L33: 0.1296 L12: -0.8018 REMARK 3 L13: 0.2673 L23: -0.0324 REMARK 3 S TENSOR REMARK 3 S11: 0.2073 S12: 0.3178 S13: -0.2196 REMARK 3 S21: -0.2063 S22: -0.1554 S23: 0.1292 REMARK 3 S31: 0.1055 S32: -0.0410 S33: -0.0435 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 38:50) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2479 1.9920 10.2869 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.1805 REMARK 3 T33: 0.0907 T12: 0.0772 REMARK 3 T13: 0.0075 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.1955 L22: 1.7106 REMARK 3 L33: 0.1144 L12: -0.5113 REMARK 3 L13: 0.2119 L23: -0.1472 REMARK 3 S TENSOR REMARK 3 S11: 0.2683 S12: 0.4387 S13: -0.0146 REMARK 3 S21: -0.4265 S22: -0.2577 S23: -0.0827 REMARK 3 S31: 0.0829 S32: 0.1729 S33: 0.0180 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 51:125) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8414 -0.2184 12.1229 REMARK 3 T TENSOR REMARK 3 T11: 0.1003 T22: 0.1542 REMARK 3 T33: 0.0744 T12: 0.0603 REMARK 3 T13: 0.0155 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.2517 L22: 1.0450 REMARK 3 L33: 0.7809 L12: -0.6202 REMARK 3 L13: 0.2746 L23: -0.0929 REMARK 3 S TENSOR REMARK 3 S11: 0.1937 S12: 0.3032 S13: 0.0430 REMARK 3 S21: -0.1675 S22: -0.1937 S23: -0.1160 REMARK 3 S31: 0.0719 S32: 0.1610 S33: 0.0084 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 126:138) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9093 4.9651 33.3032 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.1327 REMARK 3 T33: 0.1041 T12: 0.0356 REMARK 3 T13: -0.0194 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 1.3445 L22: 1.0699 REMARK 3 L33: 0.3050 L12: -0.3565 REMARK 3 L13: -0.0786 L23: 0.5540 REMARK 3 S TENSOR REMARK 3 S11: -0.1348 S12: -0.2379 S13: 0.0012 REMARK 3 S21: 0.2346 S22: 0.2009 S23: -0.0841 REMARK 3 S31: 0.0331 S32: 0.1125 S33: -0.0363 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 139:156) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9410 -9.9372 14.3779 REMARK 3 T TENSOR REMARK 3 T11: 0.1660 T22: 0.1136 REMARK 3 T33: 0.2239 T12: 0.0212 REMARK 3 T13: -0.0752 T23: -0.0659 REMARK 3 L TENSOR REMARK 3 L11: 3.8091 L22: 0.1016 REMARK 3 L33: 3.7209 L12: -0.2789 REMARK 3 L13: 2.5724 L23: 0.1573 REMARK 3 S TENSOR REMARK 3 S11: 0.3376 S12: 0.2096 S13: -0.7162 REMARK 3 S21: -0.2845 S22: 0.0341 S23: 0.3307 REMARK 3 S31: 0.4574 S32: -0.0270 S33: -0.3427 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 157:232) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8245 -5.1328 29.4904 REMARK 3 T TENSOR REMARK 3 T11: 0.1028 T22: 0.0747 REMARK 3 T33: 0.0989 T12: 0.0131 REMARK 3 T13: 0.0117 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.0334 L22: 0.6133 REMARK 3 L33: 0.6303 L12: -0.6484 REMARK 3 L13: 0.2174 L23: -0.1354 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: -0.0958 S13: -0.1723 REMARK 3 S21: 0.0971 S22: 0.0477 S23: 0.1027 REMARK 3 S31: 0.0987 S32: -0.0150 S33: -0.0309 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN H AND RESID 233:246) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1090 8.8898 21.8626 REMARK 3 T TENSOR REMARK 3 T11: 0.1593 T22: 0.1634 REMARK 3 T33: 0.3065 T12: -0.0292 REMARK 3 T13: 0.0394 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 2.2036 L22: 2.8576 REMARK 3 L33: 5.7124 L12: 1.5587 REMARK 3 L13: -3.3481 L23: -3.2029 REMARK 3 S TENSOR REMARK 3 S11: 0.1961 S12: -0.0445 S13: 0.5287 REMARK 3 S21: 0.0601 S22: -0.0567 S23: -0.3999 REMARK 3 S31: -0.4866 S32: 0.4337 S33: -0.1220 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0734 -1.5308 -3.4787 REMARK 3 T TENSOR REMARK 3 T11: 0.4130 T22: 0.5158 REMARK 3 T33: 0.1129 T12: 0.1811 REMARK 3 T13: 0.0370 T23: -0.1174 REMARK 3 L TENSOR REMARK 3 L11: 2.3395 L22: 3.0684 REMARK 3 L33: 0.6597 L12: 1.0841 REMARK 3 L13: -0.2456 L23: -1.3507 REMARK 3 S TENSOR REMARK 3 S11: 0.1925 S12: 0.9762 S13: -0.2212 REMARK 3 S21: -0.8188 S22: -0.1464 S23: -0.0680 REMARK 3 S31: 0.0039 S32: -0.2546 S33: -0.0385 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:3) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0690 16.7347 19.5677 REMARK 3 T TENSOR REMARK 3 T11: 0.1850 T22: 0.1090 REMARK 3 T33: 0.1984 T12: -0.0073 REMARK 3 T13: -0.0103 T23: 0.0313 REMARK 3 L TENSOR REMARK 3 L11: 2.1746 L22: 0.0097 REMARK 3 L33: 1.5829 L12: -0.0510 REMARK 3 L13: 0.4954 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: -0.1600 S12: 0.1180 S13: 0.4413 REMARK 3 S21: 0.0283 S22: -0.0179 S23: -0.3944 REMARK 3 S31: -0.5350 S32: 0.1711 S33: 0.1435 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN L AND RESID 4:12) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8671 14.5068 17.6045 REMARK 3 T TENSOR REMARK 3 T11: 0.1141 T22: 0.1052 REMARK 3 T33: 0.0997 T12: 0.0662 REMARK 3 T13: 0.0104 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.7856 L22: 1.1215 REMARK 3 L33: 0.3034 L12: -0.6292 REMARK 3 L13: -0.2030 L23: 0.3871 REMARK 3 S TENSOR REMARK 3 S11: 0.0867 S12: -0.0419 S13: -0.0229 REMARK 3 S21: -0.1488 S22: -0.1667 S23: 0.0097 REMARK 3 S31: -0.0939 S32: -0.0993 S33: 0.0576 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN L AND RESID 13:14D) REMARK 3 ORIGIN FOR THE GROUP (A): -2.703 7.199 28.075 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.1635 REMARK 3 T33: 0.1576 T12: 0.0261 REMARK 3 T13: 0.0186 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.7224 L22: 1.0077 REMARK 3 L33: 1.1832 L12: -0.8417 REMARK 3 L13: 0.1414 L23: 0.0115 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: -0.1665 S13: -0.1902 REMARK 3 S21: 0.0902 S22: 0.1013 S23: 0.2639 REMARK 3 S31: -0.0014 S32: -0.4163 S33: -0.0504 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN L AND RESID 14E:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1136 4.7959 33.9586 REMARK 3 T TENSOR REMARK 3 T11: 0.1339 T22: 0.1359 REMARK 3 T33: 0.1508 T12: 0.0245 REMARK 3 T13: 0.0514 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.8656 L22: 1.2619 REMARK 3 L33: 1.4195 L12: -0.0881 REMARK 3 L13: 1.0842 L23: 0.1090 REMARK 3 S TENSOR REMARK 3 S11: 0.0229 S12: -0.2367 S13: -0.1205 REMARK 3 S21: 0.0084 S22: 0.1042 S23: 0.0056 REMARK 3 S31: 0.0427 S32: -0.2619 S33: -0.0552 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 3RLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000065094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 105 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) : 1.00 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR REMARK 200 OPTICS : COLLIMATING MIRROR 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 : 55139 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48700 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1H8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000, 20MM SODIUM PHOSPHATE, REMARK 280 175MM SODIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K 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 35.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.70000 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: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 HOH H1070 LIES ON A SPECIAL POSITION. REMARK 375 HOH H1331 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 1H REMARK 465 PHE L 1G REMARK 465 GLY L 1F REMARK 465 SER L 1E REMARK 465 GLY L 1D REMARK 465 ASP L 14L REMARK 465 GLY L 14M REMARK 465 ARG L 15 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 GLU H 247 REMARK 465 ASN I 53 REMARK 465 GLY I 54 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 H 236 CG CD CE NZ REMARK 470 LYS H 240 CG CD CE NZ REMARK 470 GLU I 58 CG CD OE1 OE2 REMARK 470 GLN I 65 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 -90.79 -129.27 REMARK 500 TYR H 60A 82.61 -154.32 REMARK 500 ASN H 60G 80.65 -157.60 REMARK 500 HIS H 71 -61.02 -129.76 REMARK 500 ILE H 79 -60.22 -126.12 REMARK 500 ASN H 98 14.89 -140.50 REMARK 500 SER H 195 132.00 -33.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: N-(BENZYLSULFONYL)-D-ALANYL-N-(4- REMARK 630 CARBAMIMIDOYLBENZYL)-L-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 S29 H 1 REMARK 630 S29 H 2 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS DAL PRO 00S REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F68 RELATED DB: PDB REMARK 900 RELATED ID: 3RLW RELATED DB: PDB REMARK 900 RELATED ID: 1K1O RELATED DB: PDB REMARK 900 RELATED ID: 2ZQ1 RELATED DB: PDB REMARK 900 RELATED ID: 3P17 RELATED DB: PDB REMARK 900 RELATED ID: 3QTO RELATED DB: PDB REMARK 900 RELATED ID: 3RM0 RELATED DB: PDB REMARK 900 RELATED ID: 3RM2 RELATED DB: PDB REMARK 900 RELATED ID: 3RML RELATED DB: PDB REMARK 900 RELATED ID: 3RMM RELATED DB: PDB REMARK 900 RELATED ID: 3RMN RELATED DB: PDB REMARK 900 RELATED ID: 3RMO RELATED DB: PDB DBREF 3RLY L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3RLY H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3RLY I 53 65 UNP P09945 HIRV2_HIRME 60 72 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 ALA 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 13 ASN GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 3RLY ASN H 60G ASN GLYCOSYLATION SITE MODRES 3RLY TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET S29 H 1 33 HET S29 H 2 33 HET PO4 H 3 5 HET GOL H 4 6 HET NA H 5 1 HET NA H 6 1 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM S29 N-(BENZYLSULFONYL)-D-ALANYL-N-(4-CARBAMIMIDOYLBENZYL)- HETNAM 2 S29 L-PROLINAMIDE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NAG C8 H15 N O6 FORMUL 5 S29 2(C23 H29 N5 O4 S) FORMUL 7 PO4 O4 P 3- FORMUL 8 GOL C3 H8 O3 FORMUL 9 NA 2(NA 1+) FORMUL 11 HOH *347(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B TYR L 14J 1 9 HELIX 3 3 ALA H 55 CYS H 58 5 4 HELIX 4 4 PRO H 60B ASP H 60E 5 4 HELIX 5 5 THR H 60I ASN H 62 5 3 HELIX 6 6 ASP H 125 LEU H 130 1 9 HELIX 7 7 GLU H 164 SER H 171 1 8 HELIX 8 8 LYS H 185 GLY H 186C 5 5 HELIX 9 9 LEU H 234 GLY H 246 1 13 HELIX 10 10 PRO I 60 GLN I 65 5 6 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 B 7 GLN H 30 ARG H 35 0 SHEET 2 B 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33 SHEET 3 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 B 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 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 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.06 LINK ND2 ASN H 60G C1 NAG H 260G 1555 1555 1.43 LINK C GLU I 62 N TYS I 63 1555 1555 1.33 LINK C TYS I 63 N LEU I 64 1555 1555 1.33 CISPEP 1 SER H 36A PRO H 37 0 -2.78 CRYST1 70.300 71.400 72.400 90.00 100.30 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 0.014225 0.000000 0.002585 0.00000 SCALE2 0.000000 0.014006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014038 0.00000