HEADER HYDROLASE 07-DEC-16 5MLS TITLE THROMBIN MUTANT A190S IN COMPLEX WITH (S)-1-(D-PHENYLALANYL)-N-(3- TITLE 2 CHLOROBENZYL)PYRROLIDINE-2-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 SYNONYM: COAGULATION FACTOR II; COMPND 11 EC: 3.4.21.5; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: ALANINE 190 MUTATED TO SERINE; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: HIRUDIN VARIANT-2; COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: HTTP://SHOP.BACHEM.COM/H-7525.HTML CONTAINS SULFATED COMPND 19 TYROSINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 GENE: F2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PT2 A190S; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 TISSUE: BLOOD; SOURCE 17 GENE: F2; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PT2 A190S; SOURCE 23 MOL_ID: 3; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 26 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 27 ORGANISM_TAXID: 6421 KEYWDS COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 2 BLOOD CLOTTING INHIBITOR, PREORGANIZATION, GLYCOSILATION, BLOOD, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MARCA,A.SANDNER,A.HEINE,G.KLEBE REVDAT 2 13-JUN-18 5MLS 1 REMARK REVDAT 1 20-DEC-17 5MLS 0 JRNL AUTH A.MARCA,A.SANDNER,A.HEINE,G.KLEBE JRNL TITL THROMBIN MUTANTE A190S IN COMPLEX WITH JRNL TITL 2 (S)-1-((R)-2-AMINO-3,3-DIPHENYLPROPANOYL) JRNL TITL 3 -N-(4-CARBAMIMIDOYLBENZYL)PYRROLIDINE-2-CARBOXAMIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 44570 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2227 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 4.0730 - 3.2332 0.98 2688 141 0.1418 0.1628 REMARK 3 2 1.6904 - 1.6519 0.97 2633 139 0.2128 0.2548 REMARK 3 3 1.6519 - 1.6200 0.94 2480 130 0.2318 0.2876 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : 0.008 446 REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1C THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5539 16.1358 18.3132 REMARK 3 T TENSOR REMARK 3 T11: 0.1793 T22: 0.1224 REMARK 3 T33: 0.1417 T12: 0.0601 REMARK 3 T13: 0.0111 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.0046 L22: 0.0047 REMARK 3 L33: 0.0031 L12: -0.0009 REMARK 3 L13: 0.0017 L23: -0.0021 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: 0.0272 S13: -0.0071 REMARK 3 S21: -0.0126 S22: -0.0698 S23: -0.0211 REMARK 3 S31: -0.0787 S32: -0.0468 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 14B ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9687 13.1468 20.6840 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.1600 REMARK 3 T33: 0.1764 T12: 0.0695 REMARK 3 T13: 0.0119 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.0009 L22: 0.0017 REMARK 3 L33: 0.0026 L12: -0.0011 REMARK 3 L13: 0.0014 L23: -0.0001 REMARK 3 S TENSOR REMARK 3 S11: 0.0599 S12: 0.0249 S13: -0.0077 REMARK 3 S21: -0.0118 S22: -0.0094 S23: 0.0044 REMARK 3 S31: -0.0060 S32: -0.0675 S33: 0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14K ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2058 6.6169 32.8096 REMARK 3 T TENSOR REMARK 3 T11: 0.1107 T22: 0.1670 REMARK 3 T33: 0.1831 T12: 0.0425 REMARK 3 T13: 0.0287 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.0019 L22: 0.0009 REMARK 3 L33: 0.0037 L12: -0.0016 REMARK 3 L13: 0.0016 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: -0.0070 S12: -0.0357 S13: 0.0042 REMARK 3 S21: 0.0064 S22: 0.0208 S23: 0.0035 REMARK 3 S31: -0.0098 S32: -0.0257 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.7868 0.8829 17.5355 REMARK 3 T TENSOR REMARK 3 T11: 0.1727 T22: 0.1638 REMARK 3 T33: 0.1797 T12: 0.0434 REMARK 3 T13: -0.0503 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 0.0040 L22: 0.0018 REMARK 3 L33: 0.0018 L12: -0.0013 REMARK 3 L13: 0.0025 L23: -0.0025 REMARK 3 S TENSOR REMARK 3 S11: 0.1211 S12: 0.0575 S13: -0.0856 REMARK 3 S21: -0.0462 S22: -0.0944 S23: 0.0696 REMARK 3 S31: -0.0067 S32: -0.0580 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 30 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.4693 0.0685 8.6085 REMARK 3 T TENSOR REMARK 3 T11: 0.2443 T22: 0.2422 REMARK 3 T33: 0.1405 T12: 0.1917 REMARK 3 T13: 0.0021 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 0.0662 L22: 0.0265 REMARK 3 L33: 0.0854 L12: 0.0121 REMARK 3 L13: 0.0740 L23: 0.0126 REMARK 3 S TENSOR REMARK 3 S11: 0.1111 S12: 0.1983 S13: -0.0019 REMARK 3 S21: -0.1353 S22: -0.0928 S23: 0.0088 REMARK 3 S31: 0.0975 S32: 0.0718 S33: 0.0250 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 51 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5562 -1.9764 8.4675 REMARK 3 T TENSOR REMARK 3 T11: 0.2452 T22: 0.2880 REMARK 3 T33: 0.1153 T12: 0.2395 REMARK 3 T13: -0.0005 T23: -0.0330 REMARK 3 L TENSOR REMARK 3 L11: 0.0183 L22: 0.0683 REMARK 3 L33: 0.0734 L12: -0.0045 REMARK 3 L13: 0.0321 L23: -0.0497 REMARK 3 S TENSOR REMARK 3 S11: 0.1123 S12: 0.1580 S13: -0.0116 REMARK 3 S21: -0.1555 S22: -0.1256 S23: -0.0230 REMARK 3 S31: 0.0568 S32: 0.0351 S33: -0.0482 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 81 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6982 4.0478 15.9276 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.2380 REMARK 3 T33: 0.1285 T12: 0.1060 REMARK 3 T13: 0.0397 T23: 0.0404 REMARK 3 L TENSOR REMARK 3 L11: 0.0572 L22: 0.1490 REMARK 3 L33: 0.0159 L12: 0.0836 REMARK 3 L13: 0.0300 L23: 0.0494 REMARK 3 S TENSOR REMARK 3 S11: 0.1478 S12: 0.1854 S13: 0.1068 REMARK 3 S21: -0.1030 S22: -0.1813 S23: -0.1407 REMARK 3 S31: 0.0237 S32: 0.1255 S33: -0.0023 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 126 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4975 5.5473 32.4014 REMARK 3 T TENSOR REMARK 3 T11: 0.1424 T22: 0.1360 REMARK 3 T33: 0.1396 T12: 0.0244 REMARK 3 T13: -0.0028 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.0248 L22: 0.0128 REMARK 3 L33: 0.0041 L12: -0.0175 REMARK 3 L13: -0.0037 L23: 0.0017 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: 0.0218 S13: -0.0313 REMARK 3 S21: 0.0610 S22: 0.0279 S23: 0.0035 REMARK 3 S31: -0.0085 S32: 0.0592 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 141 THROUGH 197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4009 -8.1285 27.4731 REMARK 3 T TENSOR REMARK 3 T11: 0.1676 T22: 0.1270 REMARK 3 T33: 0.1863 T12: 0.0345 REMARK 3 T13: -0.0281 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.0631 L22: 0.0584 REMARK 3 L33: 0.0409 L12: -0.0264 REMARK 3 L13: -0.0461 L23: -0.0130 REMARK 3 S TENSOR REMARK 3 S11: 0.1257 S12: 0.0326 S13: -0.1841 REMARK 3 S21: -0.0674 S22: -0.0667 S23: 0.1385 REMARK 3 S31: 0.1441 S32: 0.0110 S33: -0.0116 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 198 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4596 -0.1500 27.5466 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.1204 REMARK 3 T33: 0.1497 T12: 0.0318 REMARK 3 T13: -0.0047 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.0645 L22: 0.0144 REMARK 3 L33: 0.0792 L12: -0.0280 REMARK 3 L13: 0.0152 L23: -0.0215 REMARK 3 S TENSOR REMARK 3 S11: 0.1078 S12: -0.0081 S13: -0.0512 REMARK 3 S21: -0.0637 S22: -0.0760 S23: 0.0778 REMARK 3 S31: 0.0499 S32: 0.0223 S33: 0.0262 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 231 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1745 9.3960 23.4532 REMARK 3 T TENSOR REMARK 3 T11: 0.1087 T22: 0.1574 REMARK 3 T33: 0.2418 T12: 0.0046 REMARK 3 T13: 0.0462 T23: 0.0567 REMARK 3 L TENSOR REMARK 3 L11: 0.0044 L22: 0.0017 REMARK 3 L33: 0.0015 L12: 0.0026 REMARK 3 L13: 0.0016 L23: 0.0018 REMARK 3 S TENSOR REMARK 3 S11: 0.0243 S12: 0.0011 S13: 0.0792 REMARK 3 S21: 0.0012 S22: -0.0336 S23: -0.0695 REMARK 3 S31: -0.0221 S32: -0.0071 S33: -0.0001 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 518 THROUGH 528 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6320 -0.9905 -2.6919 REMARK 3 T TENSOR REMARK 3 T11: 0.4690 T22: 0.4802 REMARK 3 T33: 0.1559 T12: 0.2215 REMARK 3 T13: 0.0244 T23: -0.0781 REMARK 3 L TENSOR REMARK 3 L11: 0.0002 L22: 0.0083 REMARK 3 L33: 0.0023 L12: -0.0014 REMARK 3 L13: 0.0000 L23: 0.0008 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: 0.0568 S13: 0.0011 REMARK 3 S21: -0.0263 S22: -0.0083 S23: -0.0019 REMARK 3 S31: -0.0130 S32: -0.0100 S33: 0.0106 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 5MLS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002595. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-16 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 43.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM DIHYDROGEN PHOSPHATE PH REMARK 280 7.5, 350 MM NACL, 27% PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 35.20850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.79850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.20850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.79850 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: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, D 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 H 402 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 -4 REMARK 465 PHE L -3 REMARK 465 GLY L -2 REMARK 465 SER L -1 REMARK 465 GLY L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G REMARK 465 GLY H 246 REMARK 465 GLU H 247 REMARK 465 GLY D 517 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 CD OE1 OE2 REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 107 NZ REMARK 470 LYS H 110 CE NZ REMARK 470 LYS H 145 CE NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 186D CD CE NZ REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 CD CE NZ REMARK 470 GLN H 244 OE1 NE2 REMARK 470 PHE H 245 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU D 521 CG CD OE1 OE2 REMARK 470 GLU D 524 CG CD OE1 OE2 REMARK 470 GLU D 525 CG CD OE1 OE2 REMARK 470 LEU D 527 CD2 REMARK 470 GLN D 528 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 -85.18 -132.28 REMARK 500 TYR H 60A 87.33 -157.67 REMARK 500 ASN H 60G 82.19 -153.42 REMARK 500 HIS H 71 -65.34 -127.80 REMARK 500 ILE H 79 -61.46 -128.97 REMARK 500 GLU H 97A -70.83 -114.48 REMARK 500 SER H 195 131.72 -35.58 REMARK 500 REMARK 500 REMARK: NULL 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 H 310 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 83.1 REMARK 620 3 HOH H 478 O 65.1 72.0 REMARK 620 4 HOH H 472 O 86.3 169.1 101.2 REMARK 620 5 PHE H 204A O 15.1 87.6 52.8 81.5 REMARK 620 6 HOH H 457 O 172.9 93.2 108.0 97.1 159.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 311 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 93.7 REMARK 620 3 HOH H 470 O 105.9 159.5 REMARK 620 4 HOH H 483 O 86.2 91.1 84.1 REMARK 620 5 HOH H 538 O 96.8 80.8 102.6 171.5 REMARK 620 6 HOH H 479 O 159.8 70.7 88.8 81.5 93.3 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-(3-CHLOROBENZYL)-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 22U H 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO C2A REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 22U H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL H 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 311 DBREF 5MLS L -4 17 UNP P00734 THRB_HUMAN 328 363 DBREF 5MLS H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 5MLS D 517 528 UNP P09945 HIRV2_HIRME 61 72 SEQADV 5MLS SER H 190 UNP P00734 ALA 563 ENGINEERED MUTATION 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 SER 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 D 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 5MLS TYS D 526 TYR MODIFIED RESIDUE HET TYS D 526 25 HET 22U H 301 27 HET DMS H 302 4 HET PO4 H 303 5 HET GOL H 304 6 HET GOL H 305 6 HET GOL H 306 6 HET GOL H 307 6 HET GOL H 308 6 HET GOL H 309 6 HET NA H 310 1 HET NA H 311 1 HETNAM TYS O-SULFO-L-TYROSINE HETNAM 22U D-PHENYLALANYL-N-(3-CHLOROBENZYL)-L-PROLINAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN 22U (2S)-1-[(2R)-2-AMINO-3-PHENYL-PROPANOYL]-N-[(3- HETSYN 2 22U CHLOROPHENYL)METHYL]PYRROLIDINE-2-CARBOXAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 22U C21 H24 CL N3 O2 FORMUL 5 DMS C2 H6 O S FORMUL 6 PO4 O4 P 3- FORMUL 7 GOL 6(C3 H8 O3) FORMUL 13 NA 2(NA 1+) FORMUL 15 HOH *189(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 PHE H 245 1 12 HELIX 10 AB1 PRO D 523 GLN D 528 5 6 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O LEU H 41 N LEU H 33 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 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 2.07 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK O LYS H 169 NA NA H 310 1555 1555 2.36 LINK O THR H 172 NA NA H 310 1555 1555 2.34 LINK O ARG H 221A NA NA H 311 1555 1555 2.29 LINK O LYS H 224 NA NA H 311 1555 1555 2.43 LINK C GLU D 525 N TYS D 526 1555 1555 1.33 LINK C TYS D 526 N LEU D 527 1555 1555 1.33 LINK NA NA H 310 O HOH H 478 1555 1555 2.95 LINK NA NA H 310 O HOH H 472 1555 1555 2.61 LINK NA NA H 311 O HOH H 470 1555 1555 2.35 LINK NA NA H 311 O HOH H 483 1555 1555 2.82 LINK NA NA H 311 O HOH H 538 1555 1555 2.32 LINK NA NA H 311 O HOH H 479 1555 1555 2.43 LINK O PHE H 204A NA NA H 310 1555 4556 2.40 LINK NA NA H 310 O HOH H 457 1555 4546 2.37 CISPEP 1 SER H 36A PRO H 37 0 -2.62 SITE 1 AC1 12 HIS H 57 TYR H 60A GLU H 97A SER H 190 SITE 2 AC1 12 SER H 195 VAL H 213 SER H 214 TRP H 215 SITE 3 AC1 12 GLY H 216 PHE H 227 HOH H 454 HOH H 499 SITE 1 AC2 4 LEU H 130 ARG H 165 PHE H 181 HOH H 437 SITE 1 AC3 8 ASN H 95 ASP H 100 ARG H 101 ARG H 175 SITE 2 AC3 8 GOL H 306 GOL H 307 HOH H 422 HOH H 471 SITE 1 AC4 6 ARG H 93 ARG H 165 ASP H 178 HIS H 230 SITE 2 AC4 6 GOL H 306 HOH H 429 SITE 1 AC5 3 ARG H 173 PHE H 204A HOH H 421 SITE 1 AC6 8 ARG H 93 ARG H 165 ILE H 176 THR H 177 SITE 2 AC6 8 ASP H 178 PO4 H 303 GOL H 304 HOH H 474 SITE 1 AC7 4 ARG H 93 ASN H 95 PO4 H 303 HOH H 406 SITE 1 AC8 6 ASP H 125 THR H 128 ASP H 170 HOH H 414 SITE 2 AC8 6 HOH H 435 HOH H 439 SITE 1 AC9 6 LEU H 41 CYS H 42 LYS H 60F GLU H 192 SITE 2 AC9 6 GLY H 193 SER H 195 SITE 1 AD1 6 LYS H 169 THR H 172 PHE H 204A HOH H 457 SITE 2 AD1 6 HOH H 472 HOH H 478 SITE 1 AD2 6 ARG H 221A LYS H 224 HOH H 470 HOH H 479 SITE 2 AD2 6 HOH H 483 HOH H 538 CRYST1 70.417 71.597 73.069 90.00 100.58 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 0.014201 0.000000 0.002652 0.00000 SCALE2 0.000000 0.013967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013922 0.00000