HEADER HYDROLASE/HYDROLASE INHIBITOR 12-SEP-12 3VXF TITLE X/N JOINT REFINEMENT OF HUMAN ALPHA-THROMBIN-BIVALIRUDIN COMPLEX PD5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: ALPHA-THROMBIN LIGHT CHAIN; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: ALPHA-THROMBIN HEAVY CHAIN; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: BIVALIRUDIN; COMPND 13 CHAIN: J; COMPND 14 FRAGMENT: C-TERMINAL; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: BIVALIRUDIN; COMPND 18 CHAIN: I; COMPND 19 FRAGMENT: N-TERMINAL; COMPND 20 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: UNIDENTIFIED; SOURCE 12 ORGANISM_TAXID: 32644; SOURCE 13 OTHER_DETAILS: ENZYMATICALLY PRODUCED FROM BIVALIRUDIN DURING THE SOURCE 14 CRYSTALLIZATION; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 18 ORGANISM_TAXID: 32644; SOURCE 19 OTHER_DETAILS: ENZYMATICALLY PRODUCED FROM BIVALIRUDIN DURING THE SOURCE 20 CRYSTALLIZATION KEYWDS SERINE PROTEASE, HYDROLYSIS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR T.YAMADA,K.KURIHARA,K.MASUMI,T.TAMADA,K.TOMOYORI,Y.OHNISHI,I.TANAKA, AUTHOR 2 R.KUROKI,N.NIIMURA REVDAT 5 20-NOV-24 3VXF 1 HETSYN REVDAT 4 29-JUL-20 3VXF 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 28-NOV-18 3VXF 1 SOURCE REMARK REVDAT 2 22-NOV-17 3VXF 1 REMARK REVDAT 1 04-SEP-13 3VXF 0 JRNL AUTH T.YAMADA,K.KURIHARA,Y.OHNISHI,T.TAMADA,K.TOMOYORI,K.MASUMI, JRNL AUTH 2 I.TANAKA,R.KUROKI,N.NIIMURA JRNL TITL NEUTRON AND X-RAY CRYSTALLOGRAPHIC ANALYSIS OF THE HUMAN JRNL TITL 2 ALPHA-THROMBIN-BIVALIRUDIN COMPLEX AT PD 5.0: PROTONATION JRNL TITL 3 STATES AND HYDRATION STRUCTURE OF THE ENZYME-PRODUCT COMPLEX JRNL REF BIOCHIM.BIOPHYS.ACTA V.1834 1532 2013 JRNL REFN ISSN 0006-3002 JRNL PMID 23712263 JRNL DOI 10.1016/J.BBAPAP.2013.05.014 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_663) 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 51136 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.720 REMARK 3 FREE R VALUE TEST SET COUNT : 1902 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 29.2321 - 3.4498 0.76 4072 206 0.1710 0.1850 REMARK 3 2 3.4498 - 2.7388 0.98 5083 241 0.1613 0.1914 REMARK 3 3 2.7388 - 2.3928 0.99 5130 186 0.1538 0.1625 REMARK 3 4 2.3928 - 2.1741 0.99 5112 186 0.1474 0.1665 REMARK 3 5 2.1741 - 2.0183 0.98 5077 185 0.1480 0.1775 REMARK 3 6 2.0183 - 1.8993 0.98 5010 183 0.1524 0.1898 REMARK 3 7 1.8993 - 1.8042 0.98 5008 182 0.1630 0.2017 REMARK 3 8 1.8042 - 1.7257 0.98 5002 182 0.1676 0.2174 REMARK 3 9 1.7257 - 1.6593 0.97 4972 181 0.1769 0.1875 REMARK 3 10 1.6593 - 1.6020 0.94 4768 170 0.1973 0.2136 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.37 REMARK 3 K_SOL : 0.43 REMARK 3 B_SOL : 53.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01670 REMARK 3 B22 (A**2) : 2.92560 REMARK 3 B33 (A**2) : -1.90890 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 73.7 REMARK 3 NUMBER OF REFLECTIONS : 8072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 404 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 44.8787 - 3.9689 0.81 2919 157 0.1810 0.2171 REMARK 3 2 3.9689 - 3.1505 0.79 2705 141 0.1785 0.2338 REMARK 3 3 3.1505 - 2.7523 0.60 2044 106 0.1940 0.2738 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 : 1.01 REMARK 3 K_SOL : 0.56 REMARK 3 B_SOL : 15.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79670 REMARK 3 B22 (A**2) : -2.71110 REMARK 3 B33 (A**2) : 1.91440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.016 5140 REMARK 3 ANGLE : 2.044 9130 REMARK 3 CHIRALITY : 0.117 350 REMARK 3 PLANARITY : 0.010 994 REMARK 3 DIHEDRAL : 17.995 1339 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3VXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENDING MAGNET, MONOCHROMATOR, REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NONE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 23-MAR-09 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-C REMARK 230 WAVELENGTH OR RANGE (A) : 2.6 REMARK 230 MONOCHROMATOR : SI(111) REMARK 230 OPTICS : MONOCHROMATOR REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : BIX-4 REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 8509 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 230 RESOLUTION RANGE LOW (A) : 100.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 230 DATA REDUNDANCY : NULL REMARK 230 R MERGE (I) : 0.13400 REMARK 230 R SYM (I) : NULL REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 4.7900 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 230 COMPLETENESS FOR SHELL (%) : 70.1 REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : 0.33000 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 <I/SIGMA(I)> FOR SHELL : 1.810 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 230 SOFTWARE USED : NONE REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTAL WAS OBTAINED BY A SITTING REMARK 280 DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) REMARK 280 PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION REMARK 280 OF THROMBIN-BIVALIRUDIN COMPLEX WAS 5MG/ML, PH 5.00, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 40.49900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.49900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.90000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, J, 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 O DOD H1100 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE BIVALIRUDIN N-TERMINUS FRAGMENT IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 THROMBIN INHIBITOR CLASS. REMARK 400 REMARK 400 THE BIVALIRUDIN C-TERMINUS FRAGMENT IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 THROMBIN INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BIVALIRUDIN N-TERMINUS FRAGMENT REMARK 400 CHAIN: J REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 400 REMARK 400 GROUP: 2 REMARK 400 NAME: BIVALIRUDIN C-TERMINUS FRAGMENT REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 GLY H 246 REMARK 465 GLU H 247 REMARK 465 PRO J 48 REMARK 465 GLY J 49 REMARK 465 GLY J 50 REMARK 465 GLY J 51 REMARK 465 GLY J 52 REMARK 465 ASN J 53 REMARK 465 GLY J 54 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 9 CD CE NZ REMARK 470 LYS L 14A CD CE NZ REMARK 470 ILE L 14K CA C O CB CG1 CG2 CD1 REMARK 470 ASN H 62 OD1 ND2 REMARK 470 ARG H 75 CD NE CZ NH1 NH2 REMARK 470 LYS H 87 CG CD CE NZ REMARK 470 ARG H 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 GLU H 127 CG CD OE1 OE2 REMARK 470 LYS H 149E CG CD CE NZ REMARK 470 ARG H 233 NE CZ NH1 NH2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 LYS H 240 CD CE NZ REMARK 470 GLN H 244 CD OE1 NE2 REMARK 470 ASP J 55 CG OD1 OD2 REMARK 470 GLU J 58 CG CD OE1 OE2 REMARK 470 LEU J 64 C O CB CG CD1 CD2 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 OXT ARG I 3 O DOD I 102 1.95 REMARK 500 OD1 ASP H 186A O DOD H 1113 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ARG L 14D NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP H 21 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 LYS H 186D CD - CE - NZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG H 221A CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG H 221A NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG H 221A NE - CZ - NH2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG I 3 NE - CZ - NH2 ANGL. DEV. = -4.6 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 PHE L 7 -86.15 -129.52 REMARK 500 ASN H 60G 87.28 -154.14 REMARK 500 HIS H 71 -60.92 -131.20 REMARK 500 ILE H 79 -62.87 -122.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VXE RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHY OF HUMAN ALPHA-THROMBIN-BIVALIRUDIN COMPLEX REMARK 900 AT PD5.0, 100K REMARK 999 REMARK 999 SEQUENCE REMARK 999 BIVALIRUDIN IS HYDROLYZED AT ARG3-PRO4 BOND DURING CRYSTALLIZATION REMARK 999 AND BECOMES TWO CHAINS. THE COMPLETE SEQUENCE OF BIVALIRUDIN IS REMARK 999 (DPN)PRPGGGGNGDFEEIPEEYL. DBREF 3VXF L 1H 17 UNP P00734 THRB_HUMAN 328 363 DBREF 3VXF H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3VXF J 48 64 PDB 3VXF 3VXF 48 64 DBREF 3VXF I 1 3 PDB 3VXF 3VXF 1 3 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 J 17 PRO GLY GLY GLY GLY ASN GLY ASP PHE GLU GLU ILE PRO SEQRES 2 J 17 GLU GLU TYR LEU SEQRES 1 I 3 DPN PRO ARG MODRES 3VXF ASN H 60G ASN GLYCOSYLATION SITE HET DPN I 1 22 HET NAG H 300 26 HETNAM DPN D-PHENYLALANINE 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 4 DPN C9 H11 N O2 FORMUL 5 NAG C8 H15 N O6 FORMUL 6 DOD *158(D2 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 PHE H 245 1 12 HELIX 10 10 PRO J 60 LEU J 64 5 5 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 B 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33 SHEET 5 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N TYR H 89 O LEU H 105 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 2.02 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.02 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H 300 1555 1555 1.74 LINK C DPN I 1 N PRO I 2 1555 1555 1.35 CISPEP 1 SER H 36A PRO H 37 0 -7.23 CRYST1 80.998 107.800 45.888 90.00 90.00 90.00 P 21 21 2 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 0.012346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021792 0.00000