HEADER HYDROLASE/HYDROLASE INHIBITOR 05-JAN-08 3BV9 TITLE STRUCTURE OF THROMBIN BOUND TO THE INHIBITOR FM19 CAVEAT 3BV9 CHIRALITY ERROR AT DAL404C. COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.5; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.4.21.5; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: FM19 INHIBITOR; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 GENE: F2; SOURCE 8 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 9 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS SERINE PROTEASE, ACUTE PHASE, BLOOD COAGULATION, GAMMA- KEYWDS 2 CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, KRINGLE, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.T.NIEMAN,F.BURKE,M.WARNOCK,Y.ZHOU,J.SWEIGERT,A.CHEN,D.RICKETTS, AUTHOR 2 B.R.LUCCHESI,Z.CHEN,E.DI CERA,J.HILFINGER,H.I.MOSBERG,A.H.SCHMAIER REVDAT 8 30-AUG-23 3BV9 1 REMARK REVDAT 7 20-OCT-21 3BV9 1 REMARK SEQADV LINK REVDAT 6 13-JUL-11 3BV9 1 VERSN REVDAT 5 24-FEB-09 3BV9 1 VERSN REVDAT 4 13-MAY-08 3BV9 1 JRNL REMARK REVDAT 3 06-MAY-08 3BV9 1 JRNL REVDAT 2 01-APR-08 3BV9 1 JRNL REVDAT 1 04-MAR-08 3BV9 0 JRNL AUTH M.T.NIEMAN,F.BURKE,M.WARNOCK,Y.ZHOU,J.SWEIGART,A.CHEN, JRNL AUTH 2 D.RICKETTS,B.R.LUCCHESI,Z.CHEN,E.DI CERA,J.HILFINGER, JRNL AUTH 3 J.S.KIM,H.I.MOSBERG,A.H.SCHMAIER JRNL TITL THROMBOSTATIN FM COMPOUNDS: DIRECT THROMBIN INHIBITORS - JRNL TITL 2 MECHANISM OF ACTION IN VITRO AND IN VIVO. JRNL REF J.THROMB.HAEMOST. V. 6 837 2008 JRNL REFN ISSN 1538-7933 JRNL PMID 18315550 JRNL DOI 10.1111/J.1538-7836.2008.02937.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.O.PINEDA,C.J.CARRELL,L.A.BUSH,S.PRASAD,S.CACCIA,Z.W.CHEN, REMARK 1 AUTH 2 F.S.MATHEWS,E.DI CERA REMARK 1 TITL MOLECULAR DISSECTION OF NA+ BINDING TO THROMBIN. REMARK 1 REF J.BIOL.CHEM. V. 279 31842 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15152000 REMARK 1 DOI 10.1074/JBC.M401756200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 254943.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 32806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1634 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4691 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 244 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2369 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 273 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-06 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 : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32820 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1SFQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 100 MM BIS/TRIS, 200 MM REMARK 280 NAI, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.23933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 122.47867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.85900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 153.09833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.61967 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.23933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 122.47867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 153.09833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 91.85900 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.61967 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 B 503 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 544 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE THROMBOSTATIN FM INHIBITOR [ROICPAF(P-ME)] IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THROMBOSTATIN FM INHIBITOR [ROICPAF(P-ME)] REMARK 400 CHAIN: C 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 GLY A 14M REMARK 465 ARG A 14N 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 B 247 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DAR C 401 N DAR C 401 CA -0.133 REMARK 500 OIC C 402 C PRO C 403 N 0.147 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 GLU B 186B N - CA - C ANGL. DEV. = -19.6 DEGREES REMARK 500 DAR C 401 CB - CG - CD ANGL. DEV. = 22.3 DEGREES REMARK 500 PRO C 403 C - N - CA ANGL. DEV. = 10.3 DEGREES REMARK 500 DAL C 404 N - CA - C ANGL. DEV. = 17.5 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 ALA A 1B -127.46 68.49 REMARK 500 PHE A 7 -89.20 -127.18 REMARK 500 TYR B 60A 86.86 -172.96 REMARK 500 ASN B 60G 96.69 178.97 REMARK 500 ILE B 79 -59.75 -126.64 REMARK 500 ARG B 97 16.24 -66.71 REMARK 500 GLU B 97A 123.05 -179.53 REMARK 500 ASN B 98 3.17 40.75 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 B 307 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221A O REMARK 620 2 LYS B 224 O 92.1 REMARK 620 3 HOH B 331 O 90.6 96.4 REMARK 620 4 HOH B 336 O 102.8 164.3 88.4 REMARK 620 5 HOH B 362 O 162.3 72.8 82.2 93.1 REMARK 620 6 HOH B 376 O 91.4 79.5 175.4 95.2 94.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 C 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF FM19 INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SFQ RELATED DB: PDB REMARK 900 FAST FORM OF THROMBIN MUTANT R(77A)A BOUND TO PPACK DBREF 3BV9 A 1C 14N UNP P00734 THRB_HUMAN 333 363 DBREF 3BV9 B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3BV9 C 401 405 PDB 3BV9 3BV9 401 405 SEQADV 3BV9 ALA B 77A UNP P00734 ARG 436 ENGINEERED MUTATION SEQRES 1 A 31 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 A 31 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 A 31 TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ALA ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 C 6 DAR OIC PRO DAL 4PH NH2 MODRES 3BV9 4PH C 405 PHE 4-METHYL-L-PHENYLALANINE HET DAR C 401 11 HET OIC C 402 11 HET DAL C 404 5 HET 4PH C 405 12 HET NH2 C 406 1 HET IOD B 302 1 HET IOD B 303 1 HET IOD B 304 1 HET NA B 307 1 HET GOL B 305 6 HET GOL B 306 6 HETNAM DAR D-ARGININE HETNAM OIC OCTAHYDROINDOLE-2-CARBOXYLIC ACID HETNAM DAL D-ALANINE HETNAM 4PH 4-METHYL-L-PHENYLALANINE HETNAM NH2 AMINO GROUP HETNAM IOD IODIDE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 DAR C6 H15 N4 O2 1+ FORMUL 3 OIC C9 H15 N O2 FORMUL 3 DAL C3 H7 N O2 FORMUL 3 4PH C10 H13 N O2 FORMUL 3 NH2 H2 N FORMUL 4 IOD 3(I 1-) FORMUL 7 NA NA 1+ FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *273(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B SER A 14I 1 8 HELIX 3 3 ALA B 55 LEU B 59 1 5 HELIX 4 4 PRO B 60B ASP B 60E 5 4 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 SER B 171 1 8 HELIX 8 8 LEU B 234 GLY B 246 1 13 SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N VAL B 138 O VAL B 158 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 TRP B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O PHE B 227 N TRP B 215 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 GLU B 39 LEU B 46 -1 O LEU B 41 N LEU B 33 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 ILE B 90 -1 N LYS B 87 O LYS B 107 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.06 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.05 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 LINK C DAR C 401 N OIC C 402 1555 1555 1.45 LINK C OIC C 402 N PRO C 403 1555 1555 1.49 LINK C PRO C 403 N DAL C 404 1555 1555 1.36 LINK O ARG B 221A NA NA B 307 1555 1555 2.48 LINK O LYS B 224 NA NA B 307 1555 1555 2.40 LINK NA NA B 307 O HOH B 331 1555 1555 2.52 LINK NA NA B 307 O HOH B 336 1555 1555 2.28 LINK NA NA B 307 O HOH B 362 1555 1555 2.34 LINK NA NA B 307 O HOH B 376 1555 1555 2.38 CISPEP 1 SER B 36A PRO B 37 0 -0.43 SITE 1 AC1 3 TRP B 148 DAL C 404 4PH C 405 SITE 1 AC2 1 HIS B 91 SITE 1 AC3 3 MET B 84 LYS B 110 HOH B 519 SITE 1 AC4 6 ARG B 221A LYS B 224 HOH B 331 HOH B 336 SITE 2 AC4 6 HOH B 362 HOH B 376 SITE 1 AC5 2 PRO B 92 TRP B 237 SITE 1 AC6 1 ASN B 60G SITE 1 AC7 23 HIS B 57 TYR B 60A TRP B 60D ASN B 98 SITE 2 AC7 23 THR B 147 TRP B 148 ILE B 174 ASP B 189 SITE 3 AC7 23 ALA B 190 CYS B 191 GLU B 192 SER B 195 SITE 4 AC7 23 VAL B 213 TRP B 215 GLY B 216 GLY B 219 SITE 5 AC7 23 GLY B 226 HOH B 322 HOH B 347 HOH B 407 SITE 6 AC7 23 HOH C 59 HOH C 77 HOH C 83 CRYST1 80.907 80.907 183.718 90.00 90.00 120.00 P 61 2 2 12 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 0.012360 0.007136 0.000000 0.00000 SCALE2 0.000000 0.014272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005443 0.00000