HEADER HYDROLASE/HYDROLASE INHIBITOR 21-APR-11 3RMM TITLE HUMAN THROMBIN IN COMPLEX WITH MI332 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, KEYWDS 3 GLYCOSYLATION, BLOOD, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.BIELA,A.HEINE,G.KLEBE REVDAT 4 01-NOV-23 3RMM 1 HETSYN REVDAT 3 29-JUL-20 3RMM 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 13-JUL-16 3RMM 1 JRNL REVDAT 1 25-APR-12 3RMM 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. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 45959 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 : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2302 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 49.5213 - 3.4037 1.00 4651 237 0.1452 0.1617 REMARK 3 2 3.4037 - 2.7017 1.00 4554 252 0.1581 0.1726 REMARK 3 3 2.7017 - 2.3602 0.99 4496 257 0.1636 0.1947 REMARK 3 4 2.3602 - 2.1444 0.99 4516 236 0.1490 0.1763 REMARK 3 5 2.1444 - 1.9907 0.98 4476 226 0.1486 0.1726 REMARK 3 6 1.9907 - 1.8733 0.96 4344 257 0.1435 0.1733 REMARK 3 7 1.8733 - 1.7795 0.95 4310 213 0.1516 0.1740 REMARK 3 8 1.7795 - 1.7020 0.92 4237 201 0.1637 0.1914 REMARK 3 9 1.7020 - 1.6365 0.90 4086 232 0.1871 0.2441 REMARK 3 10 1.6365 - 1.5800 0.88 3987 191 0.2009 0.2453 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 : 0.37 REMARK 3 B_SOL : 44.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.55540 REMARK 3 B22 (A**2) : -3.55210 REMARK 3 B33 (A**2) : -0.00330 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.14040 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 2559 REMARK 3 ANGLE : 1.081 3479 REMARK 3 CHIRALITY : 0.073 361 REMARK 3 PLANARITY : 0.005 440 REMARK 3 DIHEDRAL : 16.736 1020 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 16:37) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9684 -0.7629 12.7827 REMARK 3 T TENSOR REMARK 3 T11: 0.1370 T22: 0.1560 REMARK 3 T33: 0.1109 T12: 0.0677 REMARK 3 T13: -0.0345 T23: -0.0549 REMARK 3 L TENSOR REMARK 3 L11: 1.0600 L22: 0.6535 REMARK 3 L33: 0.2047 L12: -0.5830 REMARK 3 L13: 0.3000 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: 0.2684 S12: 0.3506 S13: -0.2652 REMARK 3 S21: -0.2646 S22: -0.1926 S23: 0.1232 REMARK 3 S31: 0.1278 S32: -0.0093 S33: -0.0773 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 38:50) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1661 3.4570 10.3938 REMARK 3 T TENSOR REMARK 3 T11: 0.1853 T22: 0.1867 REMARK 3 T33: 0.1089 T12: 0.0999 REMARK 3 T13: 0.0062 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.6641 L22: 0.9898 REMARK 3 L33: 0.0803 L12: -0.1501 REMARK 3 L13: 0.1116 L23: -0.0057 REMARK 3 S TENSOR REMARK 3 S11: 0.2216 S12: 0.4117 S13: -0.0876 REMARK 3 S21: -0.4154 S22: -0.2384 S23: -0.0442 REMARK 3 S31: 0.1141 S32: 0.1410 S33: 0.0087 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 51:168) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2169 -0.1152 16.8643 REMARK 3 T TENSOR REMARK 3 T11: 0.0926 T22: 0.1128 REMARK 3 T33: 0.0658 T12: 0.0500 REMARK 3 T13: -0.0067 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.5468 L22: 1.2683 REMARK 3 L33: 0.9528 L12: -0.8917 REMARK 3 L13: 0.3686 L23: -0.1902 REMARK 3 S TENSOR REMARK 3 S11: 0.1984 S12: 0.2266 S13: -0.0267 REMARK 3 S21: -0.1203 S22: -0.1719 S23: -0.0309 REMARK 3 S31: 0.0836 S32: 0.1331 S33: -0.0213 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 169:192) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7649 -9.5667 32.0456 REMARK 3 T TENSOR REMARK 3 T11: 0.1577 T22: 0.1135 REMARK 3 T33: 0.1523 T12: 0.0116 REMARK 3 T13: 0.0000 T23: 0.0243 REMARK 3 L TENSOR REMARK 3 L11: 0.4566 L22: 0.8418 REMARK 3 L33: 0.6163 L12: -0.5800 REMARK 3 L13: 0.1513 L23: -0.4405 REMARK 3 S TENSOR REMARK 3 S11: -0.0282 S12: -0.0889 S13: -0.2640 REMARK 3 S21: 0.0790 S22: 0.0911 S23: 0.1686 REMARK 3 S31: 0.1745 S32: 0.0258 S33: -0.0407 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 193:236) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0618 0.2253 26.8779 REMARK 3 T TENSOR REMARK 3 T11: 0.0917 T22: 0.0855 REMARK 3 T33: 0.0882 T12: 0.0252 REMARK 3 T13: 0.0034 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.0812 L22: 0.3089 REMARK 3 L33: 0.6525 L12: -0.4019 REMARK 3 L13: 0.0126 L23: -0.1387 REMARK 3 S TENSOR REMARK 3 S11: 0.0481 S12: -0.0727 S13: -0.1144 REMARK 3 S21: 0.0004 S22: -0.0166 S23: 0.0215 REMARK 3 S31: 0.0851 S32: 0.0252 S33: -0.0187 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 237:246) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3323 11.1094 19.0834 REMARK 3 T TENSOR REMARK 3 T11: 0.1962 T22: 0.2189 REMARK 3 T33: 0.3651 T12: -0.0156 REMARK 3 T13: 0.0780 T23: 0.0505 REMARK 3 L TENSOR REMARK 3 L11: 0.9904 L22: 2.1707 REMARK 3 L33: 2.9528 L12: 1.4071 REMARK 3 L13: -0.5372 L23: -1.3869 REMARK 3 S TENSOR REMARK 3 S11: 0.2650 S12: 0.1381 S13: 0.4843 REMARK 3 S21: 0.0759 S22: 0.0499 S23: -0.3086 REMARK 3 S31: -0.4388 S32: 0.4063 S33: -0.2281 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0523 -0.5185 -3.4097 REMARK 3 T TENSOR REMARK 3 T11: 0.5202 T22: 0.5924 REMARK 3 T33: 0.1194 T12: 0.2400 REMARK 3 T13: 0.0206 T23: -0.1079 REMARK 3 L TENSOR REMARK 3 L11: 1.3727 L22: 0.5689 REMARK 3 L33: 0.1556 L12: -0.1102 REMARK 3 L13: -0.1502 L23: -0.2328 REMARK 3 S TENSOR REMARK 3 S11: 0.4426 S12: 1.0188 S13: -0.1757 REMARK 3 S21: -0.7229 S22: -0.2835 S23: -0.1063 REMARK 3 S31: -0.0732 S32: 0.0728 S33: -0.1798 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:3) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6459 17.8651 19.7585 REMARK 3 T TENSOR REMARK 3 T11: 0.2069 T22: 0.1170 REMARK 3 T33: 0.2068 T12: 0.0206 REMARK 3 T13: 0.0046 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.8240 L22: 0.3608 REMARK 3 L33: 1.4170 L12: -0.5018 REMARK 3 L13: -0.0810 L23: 0.3280 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: 0.0336 S13: 0.4505 REMARK 3 S21: -0.0633 S22: 0.0186 S23: -0.5265 REMARK 3 S31: -0.5202 S32: -0.0108 S33: 0.0005 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN L AND RESID 4:14) REMARK 3 ORIGIN FOR THE GROUP (A): -2.025 10.068 24.865 REMARK 3 T TENSOR REMARK 3 T11: 0.1347 T22: 0.1356 REMARK 3 T33: 0.1201 T12: 0.0764 REMARK 3 T13: 0.0005 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.7777 L22: 0.9382 REMARK 3 L33: 0.2964 L12: -0.6926 REMARK 3 L13: -0.0122 L23: 0.2282 REMARK 3 S TENSOR REMARK 3 S11: 0.0736 S12: -0.0666 S13: 0.0018 REMARK 3 S21: -0.0392 S22: -0.1508 S23: 0.0684 REMARK 3 S31: -0.1499 S32: -0.2065 S33: 0.0729 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN L AND RESID 14A:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -2.889 10.476 25.491 REMARK 3 T TENSOR REMARK 3 T11: 0.1366 T22: 0.1755 REMARK 3 T33: 0.1610 T12: 0.0320 REMARK 3 T13: 0.0421 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.2600 L22: 0.3941 REMARK 3 L33: 2.0729 L12: -0.0238 REMARK 3 L13: 0.7009 L23: 0.0053 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: -0.2100 S13: -0.0721 REMARK 3 S21: 0.0458 S22: 0.0476 S23: 0.2284 REMARK 3 S31: 0.0513 S32: -0.3855 S33: 0.0273 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 3RMM 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_1000065118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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 : 48248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47800 REMARK 200 FOR SHELL : 3.000 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 (%): 50.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 35.05000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.05000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.55000 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: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12900 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 H1081 LIES ON A SPECIAL POSITION. REMARK 375 HOH H1101 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 -90.36 -130.20 REMARK 500 TYR H 60A 82.69 -152.65 REMARK 500 ASN H 60G 81.96 -156.39 REMARK 500 HIS H 71 -63.36 -131.16 REMARK 500 ILE H 79 -61.06 -125.96 REMARK 500 GLU H 97A -73.22 -112.34 REMARK 500 SER H 195 135.78 -37.45 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-[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 M32 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS DAL PRO 00T REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RML RELATED DB: PDB REMARK 900 RELATED ID: 3RM2 RELATED DB: PDB REMARK 900 RELATED ID: 3RM0 RELATED DB: PDB REMARK 900 RELATED ID: 3RLY RELATED DB: PDB REMARK 900 RELATED ID: 3RLW RELATED DB: PDB REMARK 900 RELATED ID: 3QTO RELATED DB: PDB REMARK 900 RELATED ID: 3RMN RELATED DB: PDB REMARK 900 RELATED ID: 3RMO RELATED DB: PDB DBREF 3RMM L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3RMM H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3RMM 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 3RMM ASN H 60G ASN GLYCOSYLATION SITE MODRES 3RMM TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET M32 H 1 33 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 M32 N-(BENZYLSULFONYL)-D-ALANYL-N-[2-(AMINOMETHYL)-5- HETNAM 2 M32 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 M32 C23 H29 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 *305(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 2.05 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 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 -2.04 CRYST1 70.100 71.100 72.700 90.00 100.40 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 0.014265 0.000000 0.002618 0.00000 SCALE2 0.000000 0.014065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013985 0.00000