HEADER HYDROLASE/HYDROLASE INHIBITOR 18-OCT-11 3U98 TITLE HUMAN THROMBIN IN COMPLEX WITH MI001 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 3U98 1 REMARK REVDAT 3 01-NOV-23 3U98 1 HETSYN REVDAT 2 29-JUL-20 3U98 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 24-OCT-12 3U98 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 56456 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 : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2856 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 22.5650 - 3.9293 0.73 2195 122 0.1779 0.1849 REMARK 3 2 3.9293 - 3.1215 0.91 2687 147 0.1459 0.1657 REMARK 3 3 3.1215 - 2.7276 0.93 2775 153 0.1650 0.2082 REMARK 3 4 2.7276 - 2.4786 0.94 2799 133 0.1714 0.1873 REMARK 3 5 2.4786 - 2.3011 0.95 2813 147 0.1636 0.2023 REMARK 3 6 2.3011 - 2.1656 0.95 2799 146 0.1578 0.2054 REMARK 3 7 2.1656 - 2.0572 0.96 2811 169 0.1576 0.1638 REMARK 3 8 2.0572 - 1.9677 0.95 2828 150 0.1520 0.1940 REMARK 3 9 1.9677 - 1.8920 0.94 2767 153 0.1550 0.1822 REMARK 3 10 1.8920 - 1.8267 0.93 2726 163 0.1579 0.1729 REMARK 3 11 1.8267 - 1.7696 0.93 2767 132 0.1473 0.1687 REMARK 3 12 1.7696 - 1.7191 0.93 2662 163 0.1548 0.1792 REMARK 3 13 1.7191 - 1.6738 0.93 2721 160 0.1555 0.1814 REMARK 3 14 1.6738 - 1.6330 0.92 2741 126 0.1566 0.1616 REMARK 3 15 1.6330 - 1.5959 0.92 2745 127 0.1627 0.1561 REMARK 3 16 1.5959 - 1.5619 0.91 2631 153 0.1681 0.2137 REMARK 3 17 1.5619 - 1.5307 0.88 2625 140 0.1809 0.1977 REMARK 3 18 1.5307 - 1.5018 0.87 2540 131 0.2066 0.2191 REMARK 3 19 1.5018 - 1.4750 0.84 2459 120 0.2216 0.2670 REMARK 3 20 1.4750 - 1.4500 0.84 2509 121 0.2295 0.2470 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 50.05 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00860 REMARK 3 B22 (A**2) : -1.58370 REMARK 3 B33 (A**2) : -0.42490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.48990 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 2504 REMARK 3 ANGLE : 1.117 3401 REMARK 3 CHIRALITY : 0.077 353 REMARK 3 PLANARITY : 0.005 432 REMARK 3 DIHEDRAL : 17.176 977 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): 7.1013 -1.5850 12.6081 REMARK 3 T TENSOR REMARK 3 T11: 0.1220 T22: 0.1387 REMARK 3 T33: 0.1143 T12: 0.0500 REMARK 3 T13: -0.0301 T23: -0.0378 REMARK 3 L TENSOR REMARK 3 L11: 0.1946 L22: 0.3348 REMARK 3 L33: 0.1355 L12: -0.1508 REMARK 3 L13: 0.0830 L23: 0.1011 REMARK 3 S TENSOR REMARK 3 S11: 0.2244 S12: 0.2133 S13: -0.2072 REMARK 3 S21: -0.1988 S22: -0.1741 S23: 0.1761 REMARK 3 S31: 0.1073 S32: -0.0462 S33: 0.0208 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 38:50) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7110 1.4956 10.3865 REMARK 3 T TENSOR REMARK 3 T11: 0.1893 T22: 0.1769 REMARK 3 T33: 0.1102 T12: 0.0739 REMARK 3 T13: -0.0024 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 0.6451 L22: 0.1993 REMARK 3 L33: 0.2323 L12: -0.1668 REMARK 3 L13: 0.0363 L23: 0.1735 REMARK 3 S TENSOR REMARK 3 S11: 0.2294 S12: 0.4292 S13: -0.0076 REMARK 3 S21: -0.3593 S22: -0.1537 S23: -0.0702 REMARK 3 S31: 0.2251 S32: 0.1410 S33: -0.0233 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 51:122) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6439 -0.3986 11.6836 REMARK 3 T TENSOR REMARK 3 T11: 0.1095 T22: 0.1758 REMARK 3 T33: 0.0882 T12: 0.0702 REMARK 3 T13: 0.0117 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.5208 L22: 0.6375 REMARK 3 L33: 0.6283 L12: 0.0155 REMARK 3 L13: 0.0001 L23: 0.1926 REMARK 3 S TENSOR REMARK 3 S11: 0.1524 S12: 0.2451 S13: -0.0008 REMARK 3 S21: -0.1401 S22: -0.1231 S23: -0.1136 REMARK 3 S31: 0.0492 S32: 0.1260 S33: 0.0010 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 123:136) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8129 6.8786 33.9204 REMARK 3 T TENSOR REMARK 3 T11: 0.1638 T22: 0.1538 REMARK 3 T33: 0.1099 T12: 0.0415 REMARK 3 T13: -0.0262 T23: -0.0378 REMARK 3 L TENSOR REMARK 3 L11: 0.6641 L22: 0.5567 REMARK 3 L33: 0.1771 L12: 0.1993 REMARK 3 L13: 0.2259 L23: 0.2151 REMARK 3 S TENSOR REMARK 3 S11: -0.1157 S12: -0.3128 S13: 0.1821 REMARK 3 S21: 0.2764 S22: 0.1209 S23: 0.0304 REMARK 3 S31: 0.0572 S32: 0.0886 S33: 0.0160 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 137:199) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9620 -8.2916 26.7366 REMARK 3 T TENSOR REMARK 3 T11: 0.1258 T22: 0.0853 REMARK 3 T33: 0.1240 T12: 0.0072 REMARK 3 T13: -0.0051 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.5922 L22: 0.7313 REMARK 3 L33: 0.3780 L12: -0.5921 REMARK 3 L13: 0.1430 L23: -0.4133 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.0187 S13: -0.2138 REMARK 3 S21: 0.0761 S22: 0.0321 S23: 0.1181 REMARK 3 S31: 0.0953 S32: -0.0131 S33: -0.0364 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 200:246) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3525 1.7054 26.0157 REMARK 3 T TENSOR REMARK 3 T11: 0.0770 T22: 0.0651 REMARK 3 T33: 0.0840 T12: 0.0105 REMARK 3 T13: 0.0096 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.8055 L22: 0.7054 REMARK 3 L33: 0.6895 L12: -0.7192 REMARK 3 L13: 0.1112 L23: -0.0008 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: -0.0608 S13: 0.0239 REMARK 3 S21: 0.0390 S22: 0.0010 S23: -0.0346 REMARK 3 S31: 0.0121 S32: 0.0445 S33: -0.0153 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9095 -1.6947 -3.0115 REMARK 3 T TENSOR REMARK 3 T11: 0.4259 T22: 0.5604 REMARK 3 T33: -0.0021 T12: 0.2486 REMARK 3 T13: 0.0988 T23: -0.1165 REMARK 3 L TENSOR REMARK 3 L11: 0.0024 L22: 0.0440 REMARK 3 L33: 0.0086 L12: -0.0061 REMARK 3 L13: -0.0033 L23: 0.0124 REMARK 3 S TENSOR REMARK 3 S11: 0.0858 S12: 0.1927 S13: -0.0080 REMARK 3 S21: -0.1648 S22: 0.0073 S23: -0.0082 REMARK 3 S31: -0.0460 S32: -0.0594 S33: 0.1398 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:3) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7853 16.9004 19.7339 REMARK 3 T TENSOR REMARK 3 T11: 0.1687 T22: 0.1288 REMARK 3 T33: 0.1884 T12: -0.0041 REMARK 3 T13: -0.0337 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.6953 L22: 0.1222 REMARK 3 L33: 0.3254 L12: -0.1289 REMARK 3 L13: 0.1985 L23: -0.1969 REMARK 3 S TENSOR REMARK 3 S11: -0.0116 S12: 0.0220 S13: 0.1768 REMARK 3 S21: 0.0715 S22: 0.0184 S23: -0.1362 REMARK 3 S31: -0.1897 S32: 0.1416 S33: 0.0183 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN L AND RESID 4:12) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9738 14.6161 17.5896 REMARK 3 T TENSOR REMARK 3 T11: 0.0623 T22: 0.0646 REMARK 3 T33: 0.1009 T12: 0.1543 REMARK 3 T13: 0.0449 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 0.1444 L22: 0.0420 REMARK 3 L33: 0.0733 L12: -0.0210 REMARK 3 L13: 0.0475 L23: -0.0207 REMARK 3 S TENSOR REMARK 3 S11: -0.0271 S12: -0.0563 S13: 0.0458 REMARK 3 S21: -0.1006 S22: -0.1054 S23: 0.0264 REMARK 3 S31: -0.0707 S32: -0.0605 S33: -0.1243 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN L AND RESID 13:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2270 5.9180 29.9045 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.1591 REMARK 3 T33: 0.1484 T12: 0.0338 REMARK 3 T13: 0.0330 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.3753 L22: 0.7870 REMARK 3 L33: 1.0741 L12: -0.0794 REMARK 3 L13: -0.5977 L23: -0.0206 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: -0.1693 S13: -0.0720 REMARK 3 S21: 0.1121 S22: 0.0927 S23: 0.2982 REMARK 3 S31: 0.0337 S32: -0.3138 S33: -0.0159 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 3U98 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_1000068465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-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 : 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 : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : COLLIMATING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59463 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45300 REMARK 200 FOR SHELL : 2.600 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 (%): 51.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 35.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.75000 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 35.75000 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 H1078 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 L 14A CG CD CE NZ REMARK 470 SER H 36A OG REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 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 -88.17 -128.07 REMARK 500 TYR H 60A 82.23 -153.19 REMARK 500 ASN H 60G 83.29 -157.16 REMARK 500 HIS H 71 -60.52 -128.67 REMARK 500 ILE H 79 -61.10 -126.68 REMARK 500 ASN H 95 79.68 -100.53 REMARK 500 ASN H 98 10.80 -142.00 REMARK 500 SER H 195 131.54 -35.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO- REMARK 630 PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]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 BJA H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS DAR PRO 00S 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: 3U9A RELATED DB: PDB DBREF 3U98 L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3U98 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3U98 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 3U98 ASN H 60G ASN GLYCOSYLATION SITE MODRES 3U98 TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET BJA H 1 39 HET PO4 H 2 5 HET NA H 3 1 HET NA H 4 1 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BJA (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO- HETNAM 2 BJA PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL) HETNAM 3 BJA METHYL]PYRROLIDINE-2-CARBOXAMIDE 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 FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NAG C8 H15 N O6 FORMUL 5 BJA C26 H36 N8 O4 S FORMUL 6 PO4 O4 P 3- FORMUL 7 NA 2(NA 1+) FORMUL 9 HOH *344(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 2.06 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 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 -2.58 CRYST1 70.300 71.500 72.200 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 0.014225 0.000000 0.002611 0.00000 SCALE2 0.000000 0.013986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014082 0.00000