HEADER HYDROLASE/HYDROLASE INHIBITOR 21-APR-11 3RML TITLE HUMAN THROMBIN IN COMPLEX WITH MI331 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, HIRUDIN, BLOOD, KEYWDS 3 GLYCOSYLATION, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.BIELA,A.HEINE,G.KLEBE REVDAT 5 06-DEC-23 3RML 1 REMARK REVDAT 4 01-NOV-23 3RML 1 HETSYN REVDAT 3 29-JUL-20 3RML 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 13-JUL-16 3RML 1 JRNL REVDAT 1 25-APR-12 3RML 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. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 47916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2389 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 35.6706 - 3.2956 0.98 4930 254 0.1468 0.1619 REMARK 3 2 3.2956 - 2.6161 0.99 4905 289 0.1652 0.2177 REMARK 3 3 2.6161 - 2.2854 0.99 4904 265 0.1602 0.1875 REMARK 3 4 2.2854 - 2.0765 0.98 4830 249 0.1531 0.1672 REMARK 3 5 2.0765 - 1.9277 0.95 4700 254 0.1498 0.1721 REMARK 3 6 1.9277 - 1.8140 0.91 4519 234 0.1535 0.1716 REMARK 3 7 1.8140 - 1.7232 0.89 4390 226 0.1561 0.1966 REMARK 3 8 1.7232 - 1.6482 0.86 4241 213 0.1786 0.2197 REMARK 3 9 1.6482 - 1.5847 0.83 4140 218 0.1998 0.2456 REMARK 3 10 1.5847 - 1.5300 0.80 3968 187 0.2204 0.2402 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 : 0.39 REMARK 3 B_SOL : 47.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.37990 REMARK 3 B22 (A**2) : -2.44100 REMARK 3 B33 (A**2) : -0.93900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.07160 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 2542 REMARK 3 ANGLE : 1.083 3453 REMARK 3 CHIRALITY : 0.075 357 REMARK 3 PLANARITY : 0.005 438 REMARK 3 DIHEDRAL : 17.032 1006 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 16:60H) REMARK 3 ORIGIN FOR THE GROUP (A): 13.776 -0.643 20.120 REMARK 3 T TENSOR REMARK 3 T11: 0.1821 T22: 0.2103 REMARK 3 T33: 0.0957 T12: 0.1242 REMARK 3 T13: -0.0183 T23: -0.0359 REMARK 3 L TENSOR REMARK 3 L11: 1.4748 L22: 0.7438 REMARK 3 L33: 0.6591 L12: -0.7749 REMARK 3 L13: 0.7989 L23: -0.5535 REMARK 3 S TENSOR REMARK 3 S11: 0.3716 S12: 0.4530 S13: -0.1147 REMARK 3 S21: -0.2760 S22: -0.3076 S23: -0.0033 REMARK 3 S31: 0.2330 S32: 0.2148 S33: -0.0557 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 60I:64) REMARK 3 ORIGIN FOR THE GROUP (A): 16.840 -10.541 24.920 REMARK 3 T TENSOR REMARK 3 T11: 0.4504 T22: 0.7357 REMARK 3 T33: 0.1745 T12: 0.4202 REMARK 3 T13: 0.0431 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.4397 L22: 0.1695 REMARK 3 L33: 0.8594 L12: -0.2170 REMARK 3 L13: -0.4980 L23: 0.3668 REMARK 3 S TENSOR REMARK 3 S11: 0.2344 S12: 0.3745 S13: -0.0616 REMARK 3 S21: -0.3262 S22: -0.4610 S23: -0.1223 REMARK 3 S31: -0.0637 S32: -0.1834 S33: 0.1869 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 65:146) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3797 2.7732 15.9184 REMARK 3 T TENSOR REMARK 3 T11: 0.1117 T22: 0.1343 REMARK 3 T33: 0.0493 T12: 0.0687 REMARK 3 T13: 0.0024 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.6719 L22: 1.1675 REMARK 3 L33: 0.9229 L12: -0.8530 REMARK 3 L13: 0.6154 L23: -0.2368 REMARK 3 S TENSOR REMARK 3 S11: 0.2095 S12: 0.2923 S13: 0.0407 REMARK 3 S21: -0.1658 S22: -0.1991 S23: -0.0568 REMARK 3 S31: 0.0982 S32: 0.2086 S33: -0.0136 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 147:184A) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2936 -7.0392 29.4405 REMARK 3 T TENSOR REMARK 3 T11: 0.1476 T22: 0.0950 REMARK 3 T33: 0.1183 T12: 0.0022 REMARK 3 T13: -0.0180 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.0591 L22: 1.1714 REMARK 3 L33: 0.5891 L12: -0.9193 REMARK 3 L13: 0.0477 L23: -0.5116 REMARK 3 S TENSOR REMARK 3 S11: 0.0402 S12: -0.0936 S13: -0.1957 REMARK 3 S21: 0.0636 S22: 0.0176 S23: 0.1527 REMARK 3 S31: 0.1352 S32: -0.0126 S33: -0.0606 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 185:186D) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2981 -10.2930 35.4790 REMARK 3 T TENSOR REMARK 3 T11: 0.3079 T22: 0.2367 REMARK 3 T33: 0.3494 T12: -0.0275 REMARK 3 T13: 0.0140 T23: 0.1381 REMARK 3 L TENSOR REMARK 3 L11: 3.4125 L22: 1.3460 REMARK 3 L33: 3.1090 L12: 1.7839 REMARK 3 L13: -0.8561 L23: 0.4961 REMARK 3 S TENSOR REMARK 3 S11: -0.1278 S12: -0.1076 S13: -0.1296 REMARK 3 S21: 0.1871 S22: 0.2778 S23: 0.1040 REMARK 3 S31: 0.6076 S32: -0.3358 S33: -0.0685 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 187:232) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3891 -1.7212 26.0930 REMARK 3 T TENSOR REMARK 3 T11: 0.1191 T22: 0.0918 REMARK 3 T33: 0.1019 T12: 0.0389 REMARK 3 T13: -0.0098 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.2375 L22: 0.3352 REMARK 3 L33: 1.2468 L12: -0.5208 REMARK 3 L13: 0.3406 L23: -0.3022 REMARK 3 S TENSOR REMARK 3 S11: 0.1349 S12: 0.0055 S13: -0.1700 REMARK 3 S21: -0.0780 S22: -0.0639 S23: 0.0901 REMARK 3 S31: 0.1894 S32: 0.0192 S33: -0.0633 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN H AND RESID 233:246) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0567 9.8133 21.7900 REMARK 3 T TENSOR REMARK 3 T11: 0.1631 T22: 0.2273 REMARK 3 T33: 0.3548 T12: -0.0058 REMARK 3 T13: 0.0540 T23: 0.0581 REMARK 3 L TENSOR REMARK 3 L11: 1.2431 L22: 2.4625 REMARK 3 L33: 4.5252 L12: 1.0552 REMARK 3 L13: -1.9041 L23: -2.3451 REMARK 3 S TENSOR REMARK 3 S11: 0.2346 S12: -0.0658 S13: 0.6131 REMARK 3 S21: 0.1079 S22: -0.1044 S23: -0.4448 REMARK 3 S31: -0.4197 S32: 0.5798 S33: -0.0410 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9189 -0.5434 -3.4133 REMARK 3 T TENSOR REMARK 3 T11: 0.5652 T22: 0.6215 REMARK 3 T33: 0.1288 T12: 0.3124 REMARK 3 T13: 0.0354 T23: -0.1052 REMARK 3 L TENSOR REMARK 3 L11: 1.6014 L22: 1.1408 REMARK 3 L33: 0.1043 L12: 0.2711 REMARK 3 L13: 0.3244 L23: -0.1307 REMARK 3 S TENSOR REMARK 3 S11: 0.3096 S12: 0.8918 S13: -0.0667 REMARK 3 S21: -0.8650 S22: -0.2135 S23: -0.0459 REMARK 3 S31: 0.1758 S32: 0.1957 S33: -0.0982 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:11) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0185 16.2432 18.3710 REMARK 3 T TENSOR REMARK 3 T11: 0.1591 T22: 0.1302 REMARK 3 T33: 0.1277 T12: 0.0619 REMARK 3 T13: 0.0071 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.3514 L22: 1.0854 REMARK 3 L33: 0.7024 L12: -1.0737 REMARK 3 L13: 0.2649 L23: -0.4147 REMARK 3 S TENSOR REMARK 3 S11: 0.0497 S12: 0.0318 S13: 0.2288 REMARK 3 S21: -0.0132 S22: -0.1790 S23: -0.1109 REMARK 3 S31: -0.3015 S32: -0.0369 S33: 0.0639 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN L AND RESID 12:14C) REMARK 3 ORIGIN FOR THE GROUP (A): -2.820 8.507 27.605 REMARK 3 T TENSOR REMARK 3 T11: 0.0950 T22: 0.1649 REMARK 3 T33: 0.1560 T12: 0.0427 REMARK 3 T13: -0.0056 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.9658 L22: 0.0678 REMARK 3 L33: 0.2012 L12: 0.2167 REMARK 3 L13: 0.4365 L23: 0.0892 REMARK 3 S TENSOR REMARK 3 S11: 0.1088 S12: -0.1192 S13: -0.1262 REMARK 3 S21: -0.0390 S22: -0.1149 S23: -0.0198 REMARK 3 S31: 0.0807 S32: -0.1755 S33: 0.0120 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN L AND RESID 14D:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0216 6.3242 33.2951 REMARK 3 T TENSOR REMARK 3 T11: 0.1579 T22: 0.2067 REMARK 3 T33: 0.1586 T12: 0.0426 REMARK 3 T13: 0.0499 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 2.6783 L22: 1.6807 REMARK 3 L33: 1.2101 L12: -1.4456 REMARK 3 L13: 1.6065 L23: -0.6885 REMARK 3 S TENSOR REMARK 3 S11: 0.0907 S12: -0.3899 S13: 0.0216 REMARK 3 S21: 0.0963 S22: 0.0597 S23: 0.2256 REMARK 3 S31: -0.3531 S32: -0.6170 S33: -0.1412 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 3RML 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_1000065117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 108 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 : NULL 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 : 50478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35700 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 (%): 50.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 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 34.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.60000 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 L1030 LIES ON A SPECIAL POSITION. REMARK 375 HOH H1253 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 SER H 36A OG REMARK 470 ASP H 186A CG OD1 OD2 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 -89.48 -129.28 REMARK 500 TYR H 60A 84.40 -153.96 REMARK 500 ASN H 60G 81.24 -159.29 REMARK 500 HIS H 71 -62.54 -129.43 REMARK 500 ILE H 79 -62.28 -124.99 REMARK 500 ASN H 98 15.54 -141.62 REMARK 500 SER H 195 134.02 -36.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: N-(BENZYLSULFONYL)GLYCYL-N-[2-(AMINOMETHYL)-5- REMARK 630 CHLOROBENZYL]-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 M31 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS GLY PRO 00T REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RLW RELATED DB: PDB REMARK 900 RELATED ID: 3RLY RELATED DB: PDB REMARK 900 RELATED ID: 3RM0 RELATED DB: PDB REMARK 900 RELATED ID: 3RM2 RELATED DB: PDB REMARK 900 RELATED ID: 1K1O RELATED DB: PDB REMARK 900 RELATED ID: 3QTO 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 3RML L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3RML H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3RML 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 3RML ASN H 60G ASN GLYCOSYLATION SITE MODRES 3RML TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET M31 H 1 32 HET GOL H 2 6 HET GOL H 3 6 HET PO4 H 4 5 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 M31 N-(BENZYLSULFONYL)GLYCYL-N-[2-(AMINOMETHYL)-5- HETNAM 2 M31 CHLOROBENZYL]-L-PROLINAMIDE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION 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 M31 C22 H27 CL N4 O4 S FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 PO4 O4 P 3- FORMUL 9 NA 2(NA 1+) FORMUL 11 HOH *297(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 LEU I 64 5 5 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 LEU H 41 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 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 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 -2.86 CRYST1 69.300 71.200 72.400 90.00 99.90 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 0.014430 0.000000 0.002518 0.00000 SCALE2 0.000000 0.014045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014021 0.00000