HEADER HYDROLASE 16-MAR-15 4UFE TITLE THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N-(2-((4- TITLE 2 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-BUTYL)-3-PHENYL-PROPANAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUES 364-621; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HIRUDIN VARIANT-2; COMPND 8 CHAIN: I; COMPND 9 FRAGMENT: RESIDUES 61-72; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: HIRUDIN (54-65) (SULFATED); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 14 CHAIN: L; COMPND 15 FRAGMENT: RESIDUES 333-361; COMPND 16 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: PURIFIED FROM HUMAN BLOOD PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 9 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 10 ORGANISM_TAXID: 6421; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: PURIFIED FROM HUMAN BLOOD PLASMA KEYWDS HYDROLASE, HYDROLASE INHIBITOR COMPLEX, SERINE PROTEASE, BLOOD KEYWDS 2 COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 3 BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, PREORGANIZATION, KEYWDS 4 GLYCOSYLATION, BLOOD EXPDTA X-RAY DIFFRACTION AUTHOR E.RUEHMANN,A.HEINE,G.KLEBE REVDAT 4 20-DEC-23 4UFE 1 HETSYN REVDAT 3 29-JUL-20 4UFE 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 02-MAR-16 4UFE 1 JRNL REVDAT 1 27-JAN-16 4UFE 0 JRNL AUTH E.H.RUHMANN,M.RUPP,M.BETZ,A.HEINE,G.KLEBE JRNL TITL BOOSTING AFFINITY BY CORRECT LIGAND PREORGANIZATION FOR THE JRNL TITL 2 S2 POCKET OF THROMBIN: A STUDY BY ISOTHERMAL TITRATION JRNL TITL 3 CALORIMETRY, MOLECULAR DYNAMICS, AND HIGH-RESOLUTION CRYSTAL JRNL TITL 4 STRUCTURES. JRNL REF CHEMMEDCHEM V. 11 309 2016 JRNL REFN ISSN 1860-7179 JRNL PMID 26762840 JRNL DOI 10.1002/CMDC.201500531 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 42961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2188 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 29.0011 - 4.0104 1.00 2881 128 0.1458 0.1539 REMARK 3 2 4.0104 - 3.1844 1.00 2773 168 0.1428 0.1698 REMARK 3 3 3.1844 - 2.7823 1.00 2788 154 0.1683 0.1821 REMARK 3 4 2.7823 - 2.5280 1.00 2772 163 0.1707 0.2048 REMARK 3 5 2.5280 - 2.3469 0.99 2766 139 0.1572 0.1798 REMARK 3 6 2.3469 - 2.2086 0.97 2707 156 0.1559 0.1879 REMARK 3 7 2.2086 - 2.0980 0.95 2639 139 0.1464 0.1647 REMARK 3 8 2.0980 - 2.0067 0.91 2536 122 0.1521 0.1662 REMARK 3 9 2.0067 - 1.9295 0.89 2468 135 0.1491 0.1910 REMARK 3 10 1.9295 - 1.8629 0.86 2404 108 0.1565 0.1730 REMARK 3 11 1.8629 - 1.8047 0.86 2395 129 0.1648 0.1977 REMARK 3 12 1.8047 - 1.7531 0.86 2341 157 0.1707 0.1870 REMARK 3 13 1.7531 - 1.7070 0.86 2432 104 0.1784 0.2119 REMARK 3 14 1.7070 - 1.6653 0.86 2320 143 0.1906 0.2282 REMARK 3 15 1.6653 - 1.6275 0.87 2420 123 0.1987 0.2414 REMARK 3 16 1.6275 - 1.5928 0.77 2131 120 0.2247 0.2637 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 2507 REMARK 3 ANGLE : 1.078 3392 REMARK 3 CHIRALITY : 0.044 354 REMARK 3 PLANARITY : 0.005 432 REMARK 3 DIHEDRAL : 15.227 990 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1423 -0.5627 17.2746 REMARK 3 T TENSOR REMARK 3 T11: 0.0884 T22: 0.1251 REMARK 3 T33: 0.1357 T12: 0.0137 REMARK 3 T13: 0.0004 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 2.0752 L22: 5.0690 REMARK 3 L33: 1.5397 L12: -0.1678 REMARK 3 L13: 0.8006 L23: 0.1922 REMARK 3 S TENSOR REMARK 3 S11: 0.1653 S12: -0.0126 S13: -0.1990 REMARK 3 S21: 0.0191 S22: -0.1671 S23: 0.4167 REMARK 3 S31: -0.0002 S32: -0.2496 S33: 0.0040 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 30 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2163 -1.9003 8.8029 REMARK 3 T TENSOR REMARK 3 T11: 0.1915 T22: 0.2575 REMARK 3 T33: 0.1342 T12: 0.1035 REMARK 3 T13: 0.0031 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 2.3557 L22: 2.7563 REMARK 3 L33: 3.0973 L12: -0.6895 REMARK 3 L13: -0.6525 L23: 1.2242 REMARK 3 S TENSOR REMARK 3 S11: 0.2222 S12: 0.7206 S13: -0.1578 REMARK 3 S21: -0.4735 S22: -0.2355 S23: -0.0830 REMARK 3 S31: 0.2026 S32: 0.2082 S33: -0.0100 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 51 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2394 -4.0142 8.4823 REMARK 3 T TENSOR REMARK 3 T11: 0.1874 T22: 0.2355 REMARK 3 T33: 0.1202 T12: 0.0942 REMARK 3 T13: 0.0012 T23: -0.0277 REMARK 3 L TENSOR REMARK 3 L11: 0.3400 L22: 1.6019 REMARK 3 L33: 0.9546 L12: -0.4187 REMARK 3 L13: 0.4748 L23: -0.5951 REMARK 3 S TENSOR REMARK 3 S11: 0.3135 S12: 0.4003 S13: -0.0255 REMARK 3 S21: -0.3627 S22: -0.2964 S23: -0.1070 REMARK 3 S31: 0.2512 S32: 0.1678 S33: -0.0188 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 81 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9763 1.9278 15.7705 REMARK 3 T TENSOR REMARK 3 T11: 0.0993 T22: 0.1504 REMARK 3 T33: 0.1201 T12: 0.0187 REMARK 3 T13: 0.0260 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 2.0768 L22: 1.1142 REMARK 3 L33: 1.2208 L12: -0.9675 REMARK 3 L13: 0.4068 L23: 0.0910 REMARK 3 S TENSOR REMARK 3 S11: 0.1538 S12: 0.2889 S13: 0.1657 REMARK 3 S21: -0.1010 S22: -0.1436 S23: -0.1849 REMARK 3 S31: -0.0397 S32: 0.2501 S33: -0.0115 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 126 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5172 3.7849 32.1625 REMARK 3 T TENSOR REMARK 3 T11: 0.1365 T22: 0.1419 REMARK 3 T33: 0.1286 T12: 0.0281 REMARK 3 T13: 0.0011 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 2.6910 L22: 1.7472 REMARK 3 L33: 2.3128 L12: -0.6093 REMARK 3 L13: 0.1847 L23: -0.2228 REMARK 3 S TENSOR REMARK 3 S11: -0.0959 S12: -0.3467 S13: 0.1519 REMARK 3 S21: 0.2487 S22: 0.1080 S23: -0.0735 REMARK 3 S31: 0.0037 S32: 0.2013 S33: 0.0004 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 141 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1141 -8.7720 19.9951 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.1022 REMARK 3 T33: 0.2016 T12: -0.0002 REMARK 3 T13: -0.0434 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 1.2321 L22: 1.7268 REMARK 3 L33: 1.2133 L12: -0.6237 REMARK 3 L13: -0.0927 L23: -0.7621 REMARK 3 S TENSOR REMARK 3 S11: 0.1540 S12: 0.0874 S13: -0.4041 REMARK 3 S21: -0.1767 S22: 0.0523 S23: 0.2443 REMARK 3 S31: 0.3350 S32: -0.0684 S33: -0.1159 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 165 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4978 -11.2448 35.9023 REMARK 3 T TENSOR REMARK 3 T11: 0.1809 T22: 0.1399 REMARK 3 T33: 0.1462 T12: 0.0390 REMARK 3 T13: -0.0170 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.2585 L22: 4.7095 REMARK 3 L33: 0.9432 L12: 0.6794 REMARK 3 L13: -0.5662 L23: -1.1157 REMARK 3 S TENSOR REMARK 3 S11: -0.0744 S12: -0.1281 S13: -0.1157 REMARK 3 S21: 0.3285 S22: 0.0837 S23: -0.1351 REMARK 3 S31: 0.0298 S32: 0.0643 S33: 0.0008 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 180 THROUGH 197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7350 -9.7412 27.8745 REMARK 3 T TENSOR REMARK 3 T11: 0.1491 T22: 0.0684 REMARK 3 T33: 0.1957 T12: 0.0185 REMARK 3 T13: 0.0141 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 4.0743 L22: 2.9248 REMARK 3 L33: 3.5279 L12: 1.2471 REMARK 3 L13: 0.0942 L23: -0.6215 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: -0.1322 S13: -0.2662 REMARK 3 S21: 0.1673 S22: 0.0325 S23: 0.3065 REMARK 3 S31: 0.3453 S32: -0.2676 S33: -0.0900 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 198 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4068 -1.9277 27.3396 REMARK 3 T TENSOR REMARK 3 T11: 0.0942 T22: 0.0807 REMARK 3 T33: 0.0978 T12: 0.0173 REMARK 3 T13: 0.0131 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.5421 L22: 1.2298 REMARK 3 L33: 1.2936 L12: -0.4938 REMARK 3 L13: 0.1698 L23: 0.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.0334 S12: -0.0884 S13: -0.1147 REMARK 3 S21: 0.0048 S22: 0.0068 S23: 0.0622 REMARK 3 S31: 0.0916 S32: -0.0192 S33: -0.0349 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 232 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.7136 7.9104 22.5464 REMARK 3 T TENSOR REMARK 3 T11: 0.1590 T22: 0.1637 REMARK 3 T33: 0.2971 T12: -0.0242 REMARK 3 T13: 0.0165 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 7.5292 L22: 5.1879 REMARK 3 L33: 4.0948 L12: 1.6302 REMARK 3 L13: -4.6441 L23: -2.6669 REMARK 3 S TENSOR REMARK 3 S11: 0.2301 S12: -0.0596 S13: 0.6998 REMARK 3 S21: -0.0444 S22: -0.1277 S23: -0.3886 REMARK 3 S31: -0.5001 S32: 0.5580 S33: -0.1596 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 555 THROUGH 565 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0099 -1.8202 -3.2710 REMARK 3 T TENSOR REMARK 3 T11: 0.4144 T22: 0.6322 REMARK 3 T33: 0.1525 T12: 0.1723 REMARK 3 T13: 0.0608 T23: -0.0820 REMARK 3 L TENSOR REMARK 3 L11: 1.1130 L22: 1.7041 REMARK 3 L33: 1.4420 L12: -0.0277 REMARK 3 L13: -0.3817 L23: 0.0023 REMARK 3 S TENSOR REMARK 3 S11: 0.2007 S12: 0.6840 S13: -0.1846 REMARK 3 S21: -0.8142 S22: -0.0274 S23: -0.1763 REMARK 3 S31: -0.0357 S32: 0.0416 S33: -0.0349 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1C THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0412 13.8217 18.2187 REMARK 3 T TENSOR REMARK 3 T11: 0.1662 T22: 0.0753 REMARK 3 T33: 0.0975 T12: 0.0539 REMARK 3 T13: 0.0478 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 5.9801 L22: 7.6636 REMARK 3 L33: 7.2176 L12: 0.2184 REMARK 3 L13: 5.0964 L23: 1.5725 REMARK 3 S TENSOR REMARK 3 S11: -0.0499 S12: 0.2546 S13: 0.2599 REMARK 3 S21: -0.1540 S22: -0.0642 S23: -0.2924 REMARK 3 S31: -0.5205 S32: 0.1310 S33: 0.1140 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 8 THROUGH 14B ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6351 11.0266 20.7145 REMARK 3 T TENSOR REMARK 3 T11: 0.1063 T22: 0.1384 REMARK 3 T33: 0.1274 T12: 0.0625 REMARK 3 T13: 0.0074 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 2.8830 L22: 3.5330 REMARK 3 L33: 6.5914 L12: -0.1145 REMARK 3 L13: -0.0350 L23: -4.7830 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: -0.0234 S13: 0.1584 REMARK 3 S21: -0.1741 S22: -0.0520 S23: 0.1905 REMARK 3 S31: -0.0975 S32: -0.2497 S33: -0.0484 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14K ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2187 4.9460 32.4242 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1388 REMARK 3 T33: 0.1464 T12: 0.0432 REMARK 3 T13: 0.0665 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 3.7329 L22: 4.6007 REMARK 3 L33: 2.0501 L12: 0.8086 REMARK 3 L13: 1.4614 L23: 0.2705 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: -0.3931 S13: 0.0744 REMARK 3 S21: 0.3016 S22: 0.0923 S23: 0.2608 REMARK 3 S31: 0.0097 S32: -0.3540 S33: -0.0140 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 4UFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 113 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 : NULL REMARK 200 OPTICS : NULL 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 : 42965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PDB ENTRY 1H8D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEE MATERIALS AND METHODS SECTION OF REMARK 280 PUBLICATION, PH 7.5 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 35.00300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.00300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.68000 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: 4150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, I, L 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 H2088 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 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 GLY I 554 REMARK 465 ASP L 15 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 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 ASP I 555 CG OD1 OD2 REMARK 470 GLU I 558 CG CD OE1 OE2 REMARK 470 GLU I 561 CG CD OE1 OE2 REMARK 470 GLN I 565 CG CD OE1 NE2 REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU I 564 O - C - N ANGL. DEV. = -17.4 DEGREES 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 TYR H 60A 86.97 -154.83 REMARK 500 ASN H 60G 80.52 -159.22 REMARK 500 HIS H 71 -62.96 -127.08 REMARK 500 ILE H 79 -60.77 -126.37 REMARK 500 GLU H 97A -70.27 -117.66 REMARK 500 SER H 214 -60.18 -121.45 REMARK 500 PHE L 7 -86.09 -130.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU I 564 -26.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H2056 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH L2030 DISTANCE = 6.51 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1247 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 82.1 REMARK 620 3 PHE H 204A O 99.4 100.9 REMARK 620 4 HOH H2186 O 68.9 72.3 166.8 REMARK 620 5 HOH H2187 O 85.6 167.5 79.2 105.0 REMARK 620 6 HOH H2194 O 173.7 93.7 86.0 105.4 98.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 95.5 REMARK 620 3 HOH H2212 O 161.3 67.9 REMARK 620 4 HOH H2213 O 90.7 93.1 82.1 REMARK 620 5 HOH H2224 O 97.7 83.5 89.1 171.2 REMARK 620 6 HOH H2239 O 106.2 158.2 90.3 84.4 95.8 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UFD RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH 4-(((1-((2S)-1-((2R)-2-( REMARK 900 BENZYLSULFONYLAMINO)-3-PHENYL-PROPANOYL)PYRROLIDIN-2-YL)- 1-OXO- REMARK 900 ETHYL)AMINO)METHYL)BENZAMIDINE REMARK 900 RELATED ID: 4UFF RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -(2-((4- REMARK 900 CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-ETHYL)-N -METHYL-3-PHENYL- REMARK 900 PROPANAMIDE REMARK 900 RELATED ID: 4UFG RELATED DB: PDB REMARK 900 THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -((1S)-2- REMARK 900 ((4-CARBAMIMIDOYLPHENYL)METHYLAMINO)-1-METHYL- 2-OXO-ETHYL)-N- REMARK 900 METHYL-3-PHENYL-PROPANAMIDE ETHANE REMARK 999 REMARK 999 SEQUENCE REMARK 999 ASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY REMARK 999 RESIDUES 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON REMARK 999 DENSITY REMARK 999 RESIDUE G554 WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY DBREF 4UFE H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 4UFE I 554 565 UNP P09945 HIRV2_HIRME 61 72 DBREF 4UFE L 1C 15 UNP P00734 THRB_HUMAN 333 361 SEQRES 1 H 258 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 258 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 258 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 258 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 258 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 258 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 258 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 258 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 258 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 258 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 258 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 258 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 I 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN SEQRES 1 L 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 L 29 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 L 29 TYR ILE ASP MODRES 4UFE ASN H 60G ASN GLYCOSYLATION SITE MODRES 4UFE TYS I 563 TYR O-SULFO-L-TYROSINE HET TYS I 563 16 HET NA H1247 1 HET NA H1248 1 HET 3ZD H1249 37 HET PO4 H1250 5 HET NAG H1251 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM 3ZD (2R)-N-[(2S)-1-[(4-CARBAMIMIDOYLPHENYL)METHYLAMINO]-1- HETNAM 2 3ZD OXIDANYLIDENE-PROPAN-2-YL]-3-PHENYL-2-[(PHENYLMETHYL) HETNAM 3 3ZD SULFONYLAMINO]PROPANAMIDE HETNAM PO4 PHOSPHATE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 2 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 3ZD C27 H31 N5 O4 S FORMUL 7 PO4 O4 P 3- FORMUL 8 NAG C8 H15 N O6 FORMUL 9 HOH *289(H2 O) HELIX 1 1 ALA H 55 CYS H 58 5 4 HELIX 2 2 PRO H 60B ASP H 60E 5 4 HELIX 3 3 THR H 60I ASN H 62 5 3 HELIX 4 4 ASP H 125 LEU H 130 1 9 HELIX 5 5 GLU H 164 SER H 171 1 8 HELIX 6 6 LYS H 185 GLY H 186C 5 5 HELIX 7 7 LEU H 234 GLY H 246 1 13 HELIX 8 8 PHE L 7 SER L 11 5 5 HELIX 9 9 THR L 14B TYR L 14J 1 9 SHEET 1 HA 7 SER H 20 ASP H 21 0 SHEET 2 HA 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 HA 7 LYS H 135 GLY H 140 -1 O GLY H 136 N LEU H 160 SHEET 4 HA 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 HA 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 HA 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214 SHEET 7 HA 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 HB 7 GLN H 30 ARG H 35 0 SHEET 2 HB 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 HB 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 HB 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85 SHEET 7 HB 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67 SHEET 1 HC 2 LEU H 60 TYR H 60A 0 SHEET 2 HC 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 2 CYS H 122 CYS L 1 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 H1251 1555 1555 1.42 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 LINK O LYS H 169 NA NA H1247 1555 1555 2.38 LINK O THR H 172 NA NA H1247 1555 1555 2.35 LINK O PHE H 204A NA NA H1247 4546 1555 2.40 LINK O ARG H 221A NA NA H1248 1555 1555 2.34 LINK O LYS H 224 NA NA H1248 1555 1555 2.43 LINK NA NA H1247 O HOH H2186 1555 1555 2.73 LINK NA NA H1247 O HOH H2187 1555 1555 2.53 LINK NA NA H1247 O HOH H2194 1555 1555 2.36 LINK NA NA H1248 O HOH H2212 1555 1555 2.45 LINK NA NA H1248 O HOH H2213 1555 1555 2.64 LINK NA NA H1248 O HOH H2224 1555 1555 2.34 LINK NA NA H1248 O HOH H2239 1555 1555 2.40 CISPEP 1 SER H 36A PRO H 37 0 -3.27 CRYST1 70.006 71.360 72.524 90.00 100.50 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 0.014284 0.000000 0.002647 0.00000 SCALE2 0.000000 0.014013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014023 0.00000