HEADER HYDROLASE/HYDROLASE INHIBITOR 28-FEB-11 3QWC TITLE THROMBIN INHIBITION BY PYRIDIN DERIVATIVES 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, BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, KEYWDS 4 GLYCOSYLATION, BLOOD, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.BIELA,A.HEINE,G.KLEBE REVDAT 5 06-DEC-23 3QWC 1 REMARK REVDAT 4 01-NOV-23 3QWC 1 HETSYN REVDAT 3 29-JUL-20 3QWC 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 20-JUN-12 3QWC 1 JRNL REVDAT 1 14-MAR-12 3QWC 0 JRNL AUTH A.BIELA,M.KHAYAT,H.TAN,J.KONG,A.HEINE,D.HANGAUER,G.KLEBE JRNL TITL IMPACT OF LIGAND AND PROTEIN DESOLVATION ON LIGAND BINDING JRNL TITL 2 TO THE S1 POCKET OF THROMBIN JRNL REF J.MOL.BIOL. V. 418 350 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22366545 JRNL DOI 10.1016/J.JMB.2012.01.054 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 32908 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) : 0.154 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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 24.9012 - 3.7663 0.91 3150 165 0.1382 0.1286 REMARK 3 2 3.7663 - 2.9911 0.93 3184 176 0.1488 0.1811 REMARK 3 3 2.9911 - 2.6134 0.94 3208 161 0.1730 0.2063 REMARK 3 4 2.6134 - 2.3747 0.94 3213 156 0.1573 0.2032 REMARK 3 5 2.3747 - 2.2046 0.94 3220 158 0.1496 0.1677 REMARK 3 6 2.2046 - 2.0747 0.94 3180 159 0.1450 0.1889 REMARK 3 7 2.0747 - 1.9708 0.92 3154 174 0.1477 0.1857 REMARK 3 8 1.9708 - 1.8851 0.91 3067 174 0.1627 0.1886 REMARK 3 9 1.8851 - 1.8125 0.88 2952 182 0.1865 0.2404 REMARK 3 10 1.8125 - 1.7500 0.86 2938 137 0.2063 0.2572 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 : 0.38 REMARK 3 B_SOL : 46.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.73680 REMARK 3 B22 (A**2) : -2.96610 REMARK 3 B33 (A**2) : 0.22930 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.52260 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 : 0.010 2495 REMARK 3 ANGLE : 1.070 3370 REMARK 3 CHIRALITY : 0.075 352 REMARK 3 PLANARITY : 0.005 431 REMARK 3 DIHEDRAL : 17.250 980 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 16:37) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8750 -0.4589 12.7547 REMARK 3 T TENSOR REMARK 3 T11: 0.1390 T22: 0.1590 REMARK 3 T33: 0.1101 T12: 0.0613 REMARK 3 T13: -0.0445 T23: -0.0561 REMARK 3 L TENSOR REMARK 3 L11: 0.7373 L22: 0.6049 REMARK 3 L33: 0.2879 L12: -0.5046 REMARK 3 L13: 0.3468 L23: -0.0984 REMARK 3 S TENSOR REMARK 3 S11: 0.2957 S12: 0.2855 S13: -0.2440 REMARK 3 S21: -0.2922 S22: -0.2012 S23: 0.1533 REMARK 3 S31: 0.1535 S32: 0.0199 S33: -0.1025 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 38:50) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6096 2.6302 10.5306 REMARK 3 T TENSOR REMARK 3 T11: 0.2284 T22: 0.1883 REMARK 3 T33: 0.1035 T12: 0.1013 REMARK 3 T13: 0.0023 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.5766 L22: 0.7614 REMARK 3 L33: 0.1446 L12: -0.0826 REMARK 3 L13: -0.1568 L23: -0.2177 REMARK 3 S TENSOR REMARK 3 S11: 0.2062 S12: 0.3665 S13: -0.0399 REMARK 3 S21: -0.5665 S22: -0.2885 S23: -0.0417 REMARK 3 S31: 0.1909 S32: 0.2259 S33: 0.0627 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 51:97A) REMARK 3 ORIGIN FOR THE GROUP (A): 14.392 -0.719 21.305 REMARK 3 T TENSOR REMARK 3 T11: 0.1563 T22: 0.2242 REMARK 3 T33: 0.0924 T12: 0.1187 REMARK 3 T13: 0.0177 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.6158 L22: 1.3492 REMARK 3 L33: 0.4191 L12: -0.3501 REMARK 3 L13: 0.1325 L23: 0.1209 REMARK 3 S TENSOR REMARK 3 S11: 0.3240 S12: 0.4270 S13: -0.0361 REMARK 3 S21: -0.3303 S22: -0.2850 S23: -0.1775 REMARK 3 S31: 0.1760 S32: 0.2969 S33: -0.0295 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN H AND RESID 98:143) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4620 6.0674 21.3482 REMARK 3 T TENSOR REMARK 3 T11: 0.0668 T22: 0.0669 REMARK 3 T33: 0.0534 T12: 0.0186 REMARK 3 T13: -0.0080 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.1984 L22: 0.9903 REMARK 3 L33: 0.4782 L12: -0.8707 REMARK 3 L13: -0.0267 L23: -0.1091 REMARK 3 S TENSOR REMARK 3 S11: 0.0775 S12: 0.0707 S13: 0.1190 REMARK 3 S21: -0.0394 S22: -0.1012 S23: -0.1042 REMARK 3 S31: 0.0143 S32: 0.0906 S33: 0.0140 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN H AND RESID 144:170) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4563 -7.3681 25.7980 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.0629 REMARK 3 T33: 0.1826 T12: 0.0056 REMARK 3 T13: -0.0544 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.9444 L22: 0.6678 REMARK 3 L33: 1.0712 L12: -0.6387 REMARK 3 L13: 0.3190 L23: -0.5474 REMARK 3 S TENSOR REMARK 3 S11: 0.1858 S12: -0.0654 S13: -0.4041 REMARK 3 S21: -0.0311 S22: 0.0698 S23: 0.3587 REMARK 3 S31: 0.3202 S32: -0.1056 S33: -0.2237 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN H AND RESID 171:186A) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3827 -8.6177 33.8208 REMARK 3 T TENSOR REMARK 3 T11: 0.1400 T22: 0.1167 REMARK 3 T33: 0.1403 T12: 0.0280 REMARK 3 T13: 0.0044 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 0.3782 L22: 0.4969 REMARK 3 L33: 0.5518 L12: -0.2214 REMARK 3 L13: -0.2256 L23: -0.1420 REMARK 3 S TENSOR REMARK 3 S11: -0.1751 S12: -0.2319 S13: -0.0601 REMARK 3 S21: 0.2625 S22: 0.1937 S23: 0.1325 REMARK 3 S31: 0.1307 S32: 0.0527 S33: 0.0117 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN H AND RESID 186B:192) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2665 -9.9019 26.5632 REMARK 3 T TENSOR REMARK 3 T11: 0.1707 T22: 0.1629 REMARK 3 T33: 0.3146 T12: -0.0464 REMARK 3 T13: 0.0343 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 1.0521 L22: 2.6023 REMARK 3 L33: 0.8561 L12: 0.2945 REMARK 3 L13: 0.8121 L23: -0.5005 REMARK 3 S TENSOR REMARK 3 S11: 0.1930 S12: -0.1405 S13: -0.1908 REMARK 3 S21: -0.3801 S22: 0.0500 S23: 0.1718 REMARK 3 S31: 0.3772 S32: -0.1941 S33: -0.2264 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN H AND RESID 193:234) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5041 0.1354 26.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.0917 T22: 0.0753 REMARK 3 T33: 0.0919 T12: 0.0206 REMARK 3 T13: 0.0044 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.2020 L22: 0.2447 REMARK 3 L33: 0.7771 L12: -0.4795 REMARK 3 L13: 0.1515 L23: -0.1801 REMARK 3 S TENSOR REMARK 3 S11: 0.0277 S12: -0.0758 S13: -0.1107 REMARK 3 S21: 0.0543 S22: -0.0203 S23: 0.0820 REMARK 3 S31: 0.1004 S32: 0.0267 S33: -0.0141 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN H AND RESID 235:246) REMARK 3 ORIGIN FOR THE GROUP (A): 27.8763 11.1345 20.3430 REMARK 3 T TENSOR REMARK 3 T11: 0.1836 T22: 0.1966 REMARK 3 T33: 0.4084 T12: -0.0264 REMARK 3 T13: 0.0385 T23: 0.0467 REMARK 3 L TENSOR REMARK 3 L11: 0.3217 L22: 1.9256 REMARK 3 L33: 1.3718 L12: 0.3812 REMARK 3 L13: 0.2487 L23: -0.7448 REMARK 3 S TENSOR REMARK 3 S11: 0.3145 S12: 0.0891 S13: 0.3517 REMARK 3 S21: 0.1564 S22: -0.1593 S23: -0.5249 REMARK 3 S31: -0.2966 S32: 0.3955 S33: -0.0747 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN I AND RESID 555:565) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9369 -0.4074 -3.2383 REMARK 3 T TENSOR REMARK 3 T11: 0.5756 T22: 0.5425 REMARK 3 T33: 0.0824 T12: 0.2837 REMARK 3 T13: 0.0043 T23: -0.1126 REMARK 3 L TENSOR REMARK 3 L11: 2.3851 L22: 0.8795 REMARK 3 L33: 0.0317 L12: 0.0938 REMARK 3 L13: -0.1936 L23: -0.0176 REMARK 3 S TENSOR REMARK 3 S11: 0.3797 S12: 1.0561 S13: -0.0902 REMARK 3 S21: -0.6187 S22: -0.2334 S23: 0.0034 REMARK 3 S31: 0.1794 S32: -0.0062 S33: -0.1955 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:7) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9419 15.7941 18.2305 REMARK 3 T TENSOR REMARK 3 T11: 0.1589 T22: 0.0985 REMARK 3 T33: 0.1397 T12: 0.0525 REMARK 3 T13: 0.0092 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.2509 L22: 0.1729 REMARK 3 L33: 0.5841 L12: -0.1980 REMARK 3 L13: -0.1068 L23: -0.0111 REMARK 3 S TENSOR REMARK 3 S11: 0.1617 S12: 0.0653 S13: 0.1866 REMARK 3 S21: -0.2138 S22: -0.1772 S23: -0.0866 REMARK 3 S31: -0.3726 S32: 0.0434 S33: 0.0905 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN L AND RESID 8:14) REMARK 3 ORIGIN FOR THE GROUP (A): -2.476 9.759 26.837 REMARK 3 T TENSOR REMARK 3 T11: 0.1056 T22: 0.1308 REMARK 3 T33: 0.1339 T12: 0.0710 REMARK 3 T13: -0.0026 T23: -0.0213 REMARK 3 L TENSOR REMARK 3 L11: 1.3860 L22: 0.6471 REMARK 3 L33: 0.3095 L12: -0.5123 REMARK 3 L13: 0.4528 L23: -0.0585 REMARK 3 S TENSOR REMARK 3 S11: 0.1460 S12: -0.1203 S13: -0.0176 REMARK 3 S21: -0.0359 S22: -0.0962 S23: 0.0968 REMARK 3 S31: -0.1463 S32: -0.2351 S33: 0.0337 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN L AND RESID 14A:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -3.008 10.546 25.522 REMARK 3 T TENSOR REMARK 3 T11: 0.1044 T22: 0.1588 REMARK 3 T33: 0.1655 T12: 0.0227 REMARK 3 T13: 0.0322 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.0622 L22: 0.8181 REMARK 3 L33: 1.2877 L12: 0.0163 REMARK 3 L13: 0.2204 L23: -0.3248 REMARK 3 S TENSOR REMARK 3 S11: -0.0534 S12: -0.2007 S13: -0.0851 REMARK 3 S21: 0.0420 S22: 0.1047 S23: 0.3701 REMARK 3 S31: 0.0362 S32: -0.4175 S33: 0.0059 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 3QWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-08 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 : 34739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40700 REMARK 200 FOR SHELL : 2.500 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 (%): 51.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 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 35.30000 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 35.30000 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: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 H3206 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 553 REMARK 465 GLY I 554 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 GLU I 558 CG CD OE1 OE2 REMARK 470 GLN I 565 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH L 3039 O HOH H 3059 2.08 REMARK 500 O HOH H 3245 O HOH H 3253 2.17 REMARK 500 O HOH H 3229 O HOH H 3234 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 -86.51 -128.93 REMARK 500 TYR H 60A 82.36 -157.94 REMARK 500 ASN H 60G 84.24 -157.42 REMARK 500 HIS H 71 -59.97 -130.95 REMARK 500 ILE H 79 -60.19 -126.56 REMARK 500 GLU H 97A -75.76 -115.99 REMARK 500 SER H 195 136.91 -37.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(4-CHLORO-1-METHYLPYRIDINIUM-3-YL) REMARK 630 METHYL]-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 98P H 2001 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO NNT REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F68 RELATED DB: PDB REMARK 900 RELATED ID: 1K22 RELATED DB: PDB REMARK 900 RELATED ID: 3P17 RELATED DB: PDB REMARK 900 RELATED ID: 3EQ0 RELATED DB: PDB REMARK 900 RELATED ID: 3QTO RELATED DB: PDB REMARK 900 RELATED ID: 3QTV RELATED DB: PDB REMARK 900 RELATED ID: 3QX5 RELATED DB: PDB DBREF 3QWC L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3QWC H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3QWC I 553 565 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 3QWC ASN H 60G ASN GLYCOSYLATION SITE MODRES 3QWC TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NAG H 260G 14 HET NA H1001 1 HET NA H1002 1 HET GOL H1501 6 HET 98P H2001 28 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM 98P D-PHENYLALANYL-N-[(4-CHLORO-1-METHYLPYRIDINIUM-3-YL) HETNAM 2 98P METHYL]-L-PROLINAMIDE 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 NA 2(NA 1+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 98P C21 H26 CL N4 O2 1+ FORMUL 9 HOH *259(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 560 GLN I 565 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 GLU H 39 N ARG H 35 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 2.04 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 1.46 LINK C GLU I 562 N TYS I 563 1555 1555 1.33 LINK C TYS I 563 N LEU I 564 1555 1555 1.33 CISPEP 1 SER H 36A PRO H 37 0 -4.09 CRYST1 70.600 71.500 72.700 90.00 100.60 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 0.014164 0.000000 0.002651 0.00000 SCALE2 0.000000 0.013986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013994 0.00000