HEADER HYDROLASE/HYDROLASE INHIBITOR 17-JUN-11 3SI3 TITLE HUMAN THROMBIN IN COMPLEX WITH UBTHR103 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 4 06-DEC-23 3SI3 1 REMARK REVDAT 3 01-NOV-23 3SI3 1 HETSYN REVDAT 2 29-JUL-20 3SI3 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 20-JUN-12 3SI3 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 47831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.7095 - 3.9838 1.00 2918 154 0.1540 0.1694 REMARK 3 2 3.9838 - 3.1626 1.00 2876 135 0.1356 0.1711 REMARK 3 3 3.1626 - 2.7630 0.99 2810 165 0.1611 0.1819 REMARK 3 4 2.7630 - 2.5105 0.99 2808 152 0.1626 0.2081 REMARK 3 5 2.5105 - 2.3306 0.99 2829 143 0.1538 0.1516 REMARK 3 6 2.3306 - 2.1932 0.98 2799 140 0.1477 0.1927 REMARK 3 7 2.1932 - 2.0834 0.98 2797 128 0.1501 0.1680 REMARK 3 8 2.0834 - 1.9927 0.98 2761 174 0.1441 0.1699 REMARK 3 9 1.9927 - 1.9160 0.96 2708 143 0.1453 0.1682 REMARK 3 10 1.9160 - 1.8499 0.95 2700 134 0.1464 0.1947 REMARK 3 11 1.8499 - 1.7920 0.93 2633 141 0.1502 0.1862 REMARK 3 12 1.7920 - 1.7408 0.91 2588 150 0.1568 0.1624 REMARK 3 13 1.7408 - 1.6950 0.91 2566 134 0.1722 0.1989 REMARK 3 14 1.6950 - 1.6536 0.90 2503 137 0.1845 0.2140 REMARK 3 15 1.6536 - 1.6160 0.88 2534 129 0.1967 0.2483 REMARK 3 16 1.6160 - 1.5816 0.84 2384 122 0.2190 0.1890 REMARK 3 17 1.5816 - 1.5500 0.78 2221 115 0.2394 0.2711 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 : 0.40 REMARK 3 B_SOL : 59.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.84080 REMARK 3 B22 (A**2) : -2.13130 REMARK 3 B33 (A**2) : -0.70950 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.52180 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 2557 REMARK 3 ANGLE : 1.091 3474 REMARK 3 CHIRALITY : 0.075 361 REMARK 3 PLANARITY : 0.005 441 REMARK 3 DIHEDRAL : 15.896 1016 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 16:157) REMARK 3 ORIGIN FOR THE GROUP (A): 14.4913 0.6088 14.3932 REMARK 3 T TENSOR REMARK 3 T11: 0.1015 T22: 0.1204 REMARK 3 T33: 0.0661 T12: 0.0518 REMARK 3 T13: -0.0055 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 0.7820 L22: 0.6065 REMARK 3 L33: 0.3880 L12: -0.5484 REMARK 3 L13: 0.2823 L23: -0.1896 REMARK 3 S TENSOR REMARK 3 S11: 0.1627 S12: 0.2087 S13: -0.0223 REMARK 3 S21: -0.1563 S22: -0.1421 S23: -0.0378 REMARK 3 S31: 0.1232 S32: 0.1195 S33: 0.0027 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 158:232) REMARK 3 ORIGIN FOR THE GROUP (A): 11.1488 -3.8566 29.6413 REMARK 3 T TENSOR REMARK 3 T11: 0.0920 T22: 0.0595 REMARK 3 T33: 0.0777 T12: 0.0165 REMARK 3 T13: 0.0027 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.5528 L22: 0.2902 REMARK 3 L33: 0.4627 L12: -0.3085 REMARK 3 L13: 0.0722 L23: -0.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.0050 S12: -0.0892 S13: -0.1297 REMARK 3 S21: 0.0605 S22: 0.0285 S23: 0.0849 REMARK 3 S31: 0.1157 S32: -0.0198 S33: -0.0160 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 233:246) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5066 9.8246 21.6345 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.1769 REMARK 3 T33: 0.2897 T12: -0.0301 REMARK 3 T13: 0.0447 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 0.1466 L22: 0.6869 REMARK 3 L33: 0.8232 L12: 0.2710 REMARK 3 L13: -0.3325 L23: -0.5035 REMARK 3 S TENSOR REMARK 3 S11: 0.0730 S12: 0.0281 S13: 0.2543 REMARK 3 S21: -0.0210 S22: -0.0448 S23: -0.2532 REMARK 3 S31: -0.1860 S32: 0.2710 S33: 0.0444 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN I AND RESID 55:65) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9617 -0.4725 -3.1366 REMARK 3 T TENSOR REMARK 3 T11: 0.3788 T22: 0.4258 REMARK 3 T33: 0.1678 T12: 0.1199 REMARK 3 T13: 0.0367 T23: -0.0728 REMARK 3 L TENSOR REMARK 3 L11: 0.0135 L22: 0.0597 REMARK 3 L33: 0.0007 L12: -0.0283 REMARK 3 L13: 0.0026 L23: -0.0054 REMARK 3 S TENSOR REMARK 3 S11: 0.0505 S12: 0.1458 S13: -0.0060 REMARK 3 S21: -0.1530 S22: 0.0104 S23: -0.0496 REMARK 3 S31: -0.0748 S32: 0.0041 S33: 0.0489 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN L AND RESID 1C:12) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5798 16.5627 18.2796 REMARK 3 T TENSOR REMARK 3 T11: 0.1091 T22: 0.0971 REMARK 3 T33: 0.1120 T12: 0.0422 REMARK 3 T13: 0.0053 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.6818 L22: 0.4274 REMARK 3 L33: 0.2667 L12: -0.1878 REMARK 3 L13: -0.0421 L23: -0.3033 REMARK 3 S TENSOR REMARK 3 S11: 0.0643 S12: 0.0288 S13: 0.0656 REMARK 3 S21: -0.0205 S22: -0.0913 S23: -0.1048 REMARK 3 S31: -0.1773 S32: -0.0015 S33: -0.0214 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN L AND RESID 13:14K) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2103 7.1031 29.6242 REMARK 3 T TENSOR REMARK 3 T11: 0.0940 T22: 0.1292 REMARK 3 T33: 0.1299 T12: 0.0257 REMARK 3 T13: 0.0252 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.1394 L22: 0.1197 REMARK 3 L33: 0.2123 L12: -0.0367 REMARK 3 L13: 0.0189 L23: -0.0425 REMARK 3 S TENSOR REMARK 3 S11: -0.0373 S12: -0.0671 S13: -0.0947 REMARK 3 S21: 0.0617 S22: 0.0770 S23: 0.1722 REMARK 3 S31: 0.0105 S32: -0.1797 S33: 0.0196 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 3SI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR REMARK 200 OPTICS : COLLIMATING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1H8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 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 35.05000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.05000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.70000 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: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 H1088 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 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 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 -88.96 -130.60 REMARK 500 TYR H 60A 84.18 -153.55 REMARK 500 ASN H 60G 82.26 -159.75 REMARK 500 HIS H 71 -61.81 -130.47 REMARK 500 ILE H 79 -61.24 -126.58 REMARK 500 SER H 195 131.63 -33.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-(PYRIDIN-2-YLMETHYL)-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 B03 H 5 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO APY REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3P17 RELATED DB: PDB REMARK 900 RELATED ID: 3QTO RELATED DB: PDB REMARK 900 RELATED ID: 3QTV RELATED DB: PDB REMARK 900 RELATED ID: 3QWC RELATED DB: PDB REMARK 900 RELATED ID: 3QX5 RELATED DB: PDB REMARK 900 RELATED ID: 3RLW RELATED DB: PDB DBREF 3SI3 L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3SI3 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3SI3 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 3SI3 ASN H 60G ASN GLYCOSYLATION SITE MODRES 3SI3 TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NAG H 260G 14 HET NA H 1 1 HET NA H 2 1 HET GOL H 3 6 HET PO4 H 4 5 HET B03 H 5 36 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM B03 D-PHENYLALANYL-N-(PYRIDIN-2-YLMETHYL)-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 PO4 O4 P 3- FORMUL 9 B03 C20 H24 N4 O2 FORMUL 10 HOH *350(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 GLN I 65 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 LEU H 41 N LEU H 33 SHEET 3 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 B 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.05 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 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 -3.17 CRYST1 70.100 71.400 72.300 90.00 100.10 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014265 0.000000 0.002541 0.00000 SCALE2 0.000000 0.014006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014049 0.00000