HEADER HYDROLASE/HYDROLASE INHIBITOR 18-OCT-11 3U9A TITLE HUMAN THROMBIN IN COMPLEX WITH MI330 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 4 06-DEC-23 3U9A 1 REMARK REVDAT 3 01-NOV-23 3U9A 1 HETSYN REVDAT 2 29-JUL-20 3U9A 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 24-OCT-12 3U9A 0 JRNL AUTH A.BIELA,F.SIELAFF,A.HEINE,T.STEINMETZER,G.KLEBE JRNL TITL THROMBIN INHIBITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 35.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 44933 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2233 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 35.7466 - 3.9797 0.97 2836 148 0.1558 0.1982 REMARK 3 2 3.9797 - 3.1594 0.99 2846 132 0.1474 0.1623 REMARK 3 3 3.1594 - 2.7602 0.99 2825 148 0.1680 0.2034 REMARK 3 4 2.7602 - 2.5079 0.99 2813 163 0.1770 0.2068 REMARK 3 5 2.5079 - 2.3282 0.99 2846 138 0.1616 0.1931 REMARK 3 6 2.3282 - 2.1909 0.98 2780 163 0.1582 0.1989 REMARK 3 7 2.1909 - 2.0812 0.97 2784 110 0.1556 0.1679 REMARK 3 8 2.0812 - 1.9906 0.96 2745 151 0.1529 0.1894 REMARK 3 9 1.9906 - 1.9140 0.95 2664 166 0.1552 0.1751 REMARK 3 10 1.9140 - 1.8480 0.93 2619 141 0.1629 0.2174 REMARK 3 11 1.8480 - 1.7902 0.92 2629 125 0.1767 0.1892 REMARK 3 12 1.7902 - 1.7390 0.90 2591 131 0.1813 0.2338 REMARK 3 13 1.7390 - 1.6932 0.87 2478 124 0.1989 0.2115 REMARK 3 14 1.6932 - 1.6519 0.87 2459 138 0.2081 0.2721 REMARK 3 15 1.6519 - 1.6144 0.85 2408 142 0.2247 0.2318 REMARK 3 16 1.6144 - 1.5800 0.83 2377 113 0.2330 0.2817 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 : 0.36 REMARK 3 B_SOL : 41.82 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.94640 REMARK 3 B22 (A**2) : -3.64780 REMARK 3 B33 (A**2) : 0.70140 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.01430 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 : 0.008 2559 REMARK 3 ANGLE : 1.087 3480 REMARK 3 CHIRALITY : 0.074 359 REMARK 3 PLANARITY : 0.005 440 REMARK 3 DIHEDRAL : 17.432 1013 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 16:85) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7266 -0.4693 9.6254 REMARK 3 T TENSOR REMARK 3 T11: 0.1936 T22: 0.2515 REMARK 3 T33: 0.0356 T12: 0.2023 REMARK 3 T13: 0.0223 T23: -0.1105 REMARK 3 L TENSOR REMARK 3 L11: 0.8018 L22: 0.4508 REMARK 3 L33: 0.3753 L12: -0.4696 REMARK 3 L13: 0.1949 L23: -0.0886 REMARK 3 S TENSOR REMARK 3 S11: 0.4955 S12: 0.7028 S13: -0.1663 REMARK 3 S21: -0.5688 S22: -0.2975 S23: 0.1822 REMARK 3 S31: 0.3144 S32: 0.0815 S33: 0.2928 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 86:129C) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5973 4.4547 19.4784 REMARK 3 T TENSOR REMARK 3 T11: 0.1417 T22: 0.1809 REMARK 3 T33: 0.1422 T12: 0.0587 REMARK 3 T13: -0.0001 T23: 0.0161 REMARK 3 L TENSOR REMARK 3 L11: 0.4149 L22: 0.2883 REMARK 3 L33: 0.2039 L12: -0.0971 REMARK 3 L13: 0.0684 L23: 0.1028 REMARK 3 S TENSOR REMARK 3 S11: 0.0860 S12: 0.1236 S13: 0.1418 REMARK 3 S21: 0.0014 S22: -0.1040 S23: -0.1695 REMARK 3 S31: -0.0372 S32: 0.1232 S33: 0.0111 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 130:176) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6607 -6.2302 27.0726 REMARK 3 T TENSOR REMARK 3 T11: 0.1728 T22: 0.1184 REMARK 3 T33: 0.1628 T12: 0.0198 REMARK 3 T13: -0.0154 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.5847 L22: 0.4349 REMARK 3 L33: 0.3309 L12: -0.4828 REMARK 3 L13: 0.0683 L23: -0.2208 REMARK 3 S TENSOR REMARK 3 S11: 0.0865 S12: -0.0259 S13: -0.2840 REMARK 3 S21: 0.0122 S22: -0.0050 S23: 0.2385 REMARK 3 S31: 0.1979 S32: -0.0068 S33: -0.0464 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 177:186D) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2020 -6.4960 33.5000 REMARK 3 T TENSOR REMARK 3 T11: 0.1945 T22: 0.1691 REMARK 3 T33: 0.2498 T12: -0.0051 REMARK 3 T13: 0.0096 T23: 0.0772 REMARK 3 L TENSOR REMARK 3 L11: 0.4180 L22: 0.2580 REMARK 3 L33: 0.5726 L12: 0.0879 REMARK 3 L13: -0.3889 L23: 0.0841 REMARK 3 S TENSOR REMARK 3 S11: -0.0420 S12: -0.2044 S13: -0.2623 REMARK 3 S21: 0.1686 S22: 0.1610 S23: 0.2503 REMARK 3 S31: 0.1712 S32: -0.0615 S33: -0.0237 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 187:238) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0693 -0.3557 26.2072 REMARK 3 T TENSOR REMARK 3 T11: 0.1066 T22: 0.0892 REMARK 3 T33: 0.1297 T12: 0.0267 REMARK 3 T13: 0.0023 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.5269 L22: 0.1249 REMARK 3 L33: 0.3717 L12: -0.2317 REMARK 3 L13: 0.0884 L23: -0.0933 REMARK 3 S TENSOR REMARK 3 S11: 0.0458 S12: -0.0744 S13: -0.1601 REMARK 3 S21: 0.0250 S22: -0.0172 S23: 0.0595 REMARK 3 S31: 0.1042 S32: -0.0019 S33: 0.0025 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 239:246) REMARK 3 ORIGIN FOR THE GROUP (A): 29.2799 12.4542 18.2972 REMARK 3 T TENSOR REMARK 3 T11: 0.2607 T22: 0.2640 REMARK 3 T33: 0.4598 T12: -0.0211 REMARK 3 T13: 0.0758 T23: 0.0715 REMARK 3 L TENSOR REMARK 3 L11: 0.0717 L22: 0.2718 REMARK 3 L33: 0.2668 L12: 0.0429 REMARK 3 L13: 0.0992 L23: -0.1187 REMARK 3 S TENSOR REMARK 3 S11: 0.0786 S12: 0.0780 S13: 0.1252 REMARK 3 S21: 0.0043 S22: -0.0080 S23: -0.1189 REMARK 3 S31: -0.1092 S32: 0.0619 S33: -0.0230 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0020 -0.5325 -3.2107 REMARK 3 T TENSOR REMARK 3 T11: 0.5024 T22: 0.5718 REMARK 3 T33: 0.0761 T12: 0.2762 REMARK 3 T13: 0.0743 T23: -0.1515 REMARK 3 L TENSOR REMARK 3 L11: 0.0564 L22: 0.0274 REMARK 3 L33: 0.0604 L12: -0.0119 REMARK 3 L13: -0.0574 L23: 0.0094 REMARK 3 S TENSOR REMARK 3 S11: 0.0940 S12: 0.0806 S13: 0.0178 REMARK 3 S21: -0.0512 S22: -0.0117 S23: -0.0211 REMARK 3 S31: -0.0287 S32: 0.0046 S33: 0.0596 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:3) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7666 17.8989 19.7130 REMARK 3 T TENSOR REMARK 3 T11: 0.2041 T22: 0.1343 REMARK 3 T33: 0.2278 T12: 0.0262 REMARK 3 T13: 0.0135 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 0.4792 L22: 0.0088 REMARK 3 L33: 0.5803 L12: 0.0371 REMARK 3 L13: -0.5275 L23: -0.0415 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.0187 S13: 0.2335 REMARK 3 S21: -0.0572 S22: -0.0611 S23: -0.1610 REMARK 3 S31: -0.1938 S32: 0.0507 S33: 0.0322 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN L AND RESID 4:14C) REMARK 3 ORIGIN FOR THE GROUP (A): -2.4535 12.4408 19.8516 REMARK 3 T TENSOR REMARK 3 T11: 0.1564 T22: 0.1760 REMARK 3 T33: 0.1710 T12: 0.0655 REMARK 3 T13: 0.0040 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.8060 L22: 0.5369 REMARK 3 L33: 0.0890 L12: -0.1669 REMARK 3 L13: 0.1641 L23: 0.0347 REMARK 3 S TENSOR REMARK 3 S11: 0.0757 S12: -0.0681 S13: -0.0194 REMARK 3 S21: -0.1333 S22: -0.0826 S23: 0.0419 REMARK 3 S31: -0.0454 S32: -0.1193 S33: 0.0340 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN L AND RESID 14D:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5052 5.9671 33.6140 REMARK 3 T TENSOR REMARK 3 T11: 0.1633 T22: 0.2261 REMARK 3 T33: 0.1953 T12: 0.0419 REMARK 3 T13: 0.0576 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 0.1884 L22: 0.0739 REMARK 3 L33: 0.1733 L12: -0.0321 REMARK 3 L13: 0.1250 L23: 0.0525 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.1307 S13: 0.0537 REMARK 3 S21: 0.0314 S22: -0.0342 S23: 0.0737 REMARK 3 S31: -0.0582 S32: -0.2096 S33: 0.0128 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 3U9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068467. 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) : 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 : 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 : 46917 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 28.8000 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 (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47100 REMARK 200 FOR SHELL : 2.400 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 (%): 50.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8000, 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 34.95000 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 34.95000 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: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 CZ ARG H 75 LIES ON A SPECIAL POSITION. REMARK 375 HOH H1195 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 ARG L 14D CG CD NE CZ NH1 NH2 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 GLU I 58 CG CD OE1 OE2 REMARK 470 GLU I 61 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 -90.35 -129.37 REMARK 500 TYR H 60A 84.20 -153.88 REMARK 500 ASN H 60G 81.49 -159.03 REMARK 500 HIS H 71 -62.62 -131.73 REMARK 500 ILE H 79 -61.95 -127.59 REMARK 500 ASN H 98 19.35 -146.26 REMARK 500 SER H 195 134.53 -37.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: (2S)-N-[[2-(AMINOMETHYL)-5-CHLORANYL-PHENYL]METHYL]- REMARK 630 1-[(2S)-2-[(3-CHLORANYL-4-METHOXY-PHENYL)SULFONYLAMINO]-4-[(4- REMARK 630 CYANOPHENYL)METHYLAMINO]-4-OXIDANYLIDENE-BUTANOYL]PYRROLIDINE-2- REMARK 630 CARBOXAMIDE 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 S33 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: BSZ AS7 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: 3RML RELATED DB: PDB REMARK 900 RELATED ID: 3RMM RELATED DB: PDB REMARK 900 RELATED ID: 3U98 RELATED DB: PDB DBREF 3U9A L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3U9A H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3U9A 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 3U9A ASN H 60G ASN GLYCOSYLATION SITE MODRES 3U9A TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET S33 H 1 47 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 S33 (2S)-N-[[2-(AMINOMETHYL)-5-CHLORANYL-PHENYL]METHYL]-1- HETNAM 2 S33 [(2S)-2-[(3-CHLORANYL-4-METHOXY-PHENYL)SULFONYLAMINO]- HETNAM 3 S33 4-[(4-CYANOPHENYL)METHYLAMINO]-4-OXIDANYLIDENE- HETNAM 4 S33 BUTANOYL]PYRROLIDINE-2-CARBOXAMIDE 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 S33 C32 H34 CL2 N6 O6 S FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 PO4 O4 P 3- FORMUL 9 NA 2(NA 1+) FORMUL 11 HOH *253(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 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 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 -1.93 CRYST1 69.900 71.200 72.600 90.00 100.10 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 0.014306 0.000000 0.002548 0.00000 SCALE2 0.000000 0.014045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013991 0.00000