HEADER HYDROLASE/HYDROLASE INHIBITOR 09-JAN-10 3LC3 TITLE BENZOTHIOPHENE INHIBITORS OF FACTOR IXA COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR IX; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RESIDUES 227-461; COMPND 5 SYNONYM: CHRISTMAS FACTOR, PLASMA THROMBOPLASTIN COMPONENT, COMPND 6 PTC, COAGULATION FACTOR IXA LIGHT CHAIN, COAGULATION FACTOR COMPND 7 IXA HEAVY CHAIN; COMPND 8 EC: 3.4.21.22; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: COAGULATION FACTOR IX; COMPND 12 CHAIN: B, D; COMPND 13 FRAGMENT: RESIDUES 133-188; COMPND 14 SYNONYM: CHRISTMAS FACTOR, PLASMA THROMBOPLASTIN COMPONENT, COMPND 15 PTC, COAGULATION FACTOR IXA LIGHT CHAIN, COAGULATION FACTOR COMPND 16 IXA HEAVY CHAIN; COMPND 17 EC: 3.4.21.22; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F9; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-INHIBITOR COMPLEX, PEPTIDASE S1, BLOOD COAGULATION, KEYWDS 2 CALCIUM, CLEAVAGE ON PAIR OF BASIC RESIDUES, DISEASE KEYWDS 3 MUTATION, DISULFIDE BOND, EGF-LIKE DOMAIN, GAMMA- KEYWDS 4 CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, HEMOPHILIA, HYDROLASE, KEYWDS 5 HYDROXYLATION, PHARMACEUTICAL, PHOSPHOPROTEIN, KEYWDS 6 POLYMORPHISM, PROTEASE, SECRETED, SERINE PROTEASE, KEYWDS 7 SULFATION, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.WANG,R.BECK REVDAT 2 02-MAR-10 3LC3 1 JRNL REVDAT 1 23-FEB-10 3LC3 0 JRNL AUTH S.WANG,R.BECK,T.BLENCH,A.BURD,S.BUXTON,M.MALIC, JRNL AUTH 2 T.AYELE,S.SHAIKH,S.CHAHWALA,C.CHANDER,R.HOLLAND, JRNL AUTH 3 S.MERETTE,L.ZHAO,M.BLACKNEY,A.WATTS JRNL TITL STUDIES OF BENZOTHIOPHENE TEMPLATE AS POTENT FACTOR JRNL TITL 2 IXA (FIXA) INHIBITORS IN THROMBOSIS. JRNL REF J.MED.CHEM. V. 53 1465 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20121198 JRNL DOI 10.1021/JM901475E REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 41605 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 + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1754 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3016 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4548 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : 1.06000 REMARK 3 B33 (A**2) : -0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.176 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.844 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4756 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4172 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6452 ; 1.481 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9714 ; 0.836 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 6.940 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;35.509 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 788 ;15.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.439 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5306 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 988 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1008 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4440 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2324 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2803 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 351 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.029 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.067 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 40 ; 0.272 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 112 ; 0.176 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 8 ; 0.111 ; 0.200 REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2978 ; 0.996 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1210 ; 0.203 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4664 ; 1.598 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2120 ; 2.064 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1788 ; 3.007 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3LC3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB057093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43359 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 67.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 48.01750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 THR B 140 REMARK 475 SER B 141 REMARK 475 LYS B 142 REMARK 475 THR D 140 REMARK 475 SER D 141 REMARK 475 LYS D 142 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 36 CD CE NZ REMARK 480 ARG A 150 CZ NH1 NH2 REMARK 480 TYR A 177 CD1 CD2 CE1 CE2 CZ OH REMARK 480 ASN A 178 CG OD1 ND2 REMARK 480 MET B 86 CG SD CE REMARK 480 LYS B 91 CD CE NZ REMARK 480 ARG B 94 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 100 CG CD CE NZ REMARK 480 ASP B 104 CG OD1 OD2 REMARK 480 ASN B 105 CG OD1 ND2 REMARK 480 LYS B 106 CG CD CE NZ REMARK 480 VAL B 107 CG1 CG2 REMARK 480 VAL B 108 CG1 CG2 REMARK 480 GLU B 119 CG CD OE1 OE2 REMARK 480 GLU B 125 CG CD OE1 OE2 REMARK 480 LYS C 36 CD CE NZ REMARK 480 ARG C 150 CZ NH1 NH2 REMARK 480 TYR C 177 CD1 CD2 CE1 CE2 CZ OH REMARK 480 ASN C 178 CG OD1 ND2 REMARK 480 MET D 86 CG SD CE REMARK 480 LYS D 91 CD CE NZ REMARK 480 ARG D 94 CG CD NE CZ NH1 NH2 REMARK 480 LYS D 100 CG CD CE NZ REMARK 480 ASP D 104 CG OD1 OD2 REMARK 480 ASN D 105 CG OD1 ND2 REMARK 480 LYS D 106 CG CD CE NZ REMARK 480 VAL D 107 CG1 CG2 REMARK 480 VAL D 108 CG1 CG2 REMARK 480 GLU D 119 CG CD OE1 OE2 REMARK 480 GLU D 125 CG CD OE1 OE2 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 NZ LYS C 23 O GLN D 139 2.10 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 ASP A 39 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 125 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP C 39 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP C 125 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP D 104 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 63 68.20 1.75 REMARK 500 HIS A 71 -65.39 -137.28 REMARK 500 LYS A 148 19.20 55.53 REMARK 500 SER A 214 -72.92 -117.68 REMARK 500 GLU A 217 -149.44 -99.03 REMARK 500 GLN B 97 -85.35 -111.66 REMARK 500 ASP B 104 -81.37 59.40 REMARK 500 ASN B 105 73.64 -68.23 REMARK 500 LYS B 106 -161.80 -77.31 REMARK 500 VAL B 107 108.51 75.03 REMARK 500 ASN B 120 -11.87 -48.92 REMARK 500 SER B 141 -83.21 -107.05 REMARK 500 HIS C 71 -62.14 -135.42 REMARK 500 SER C 214 -70.61 -118.81 REMARK 500 GLU C 217 -150.58 -101.76 REMARK 500 LYS D 91 44.93 39.76 REMARK 500 GLN D 97 -83.92 -109.55 REMARK 500 ALA D 103 94.03 -52.60 REMARK 500 ASP D 104 -51.01 71.78 REMARK 500 LYS D 106 -172.38 43.23 REMARK 500 VAL D 107 98.01 73.45 REMARK 500 ASN D 120 -49.32 -28.88 REMARK 500 LYS D 122 -51.63 -129.28 REMARK 500 SER D 141 -94.52 -124.92 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 CA A 246 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 75 O REMARK 620 2 ASN A 72 O 82.2 REMARK 620 3 GLU A 70 OE1 154.6 86.9 REMARK 620 4 GLU A 80 OE2 94.0 166.4 101.5 REMARK 620 5 GLU A 77 OE1 122.7 90.3 80.1 80.7 REMARK 620 6 GLU A 77 OE2 72.5 84.2 129.2 82.3 50.2 REMARK 620 7 HOH A 6 O 82.0 99.3 77.3 93.0 154.8 153.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 246 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN C 72 O REMARK 620 2 GLU C 75 O 80.7 REMARK 620 3 GLU C 70 OE1 87.5 154.2 REMARK 620 4 GLU C 80 OE2 170.4 97.0 98.2 REMARK 620 5 GLU C 77 OE1 87.3 122.8 79.1 86.2 REMARK 620 6 GLU C 77 OE2 86.6 72.1 130.3 83.8 51.4 REMARK 620 7 HOH C 400 O 98.2 83.5 75.6 90.8 153.7 154.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IYX A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IYX A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IYX C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IYX C 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LC5 RELATED DB: PDB DBREF 3LC3 A 16 245 UNP P00740 FA9_HUMAN 227 461 DBREF 3LC3 B 87 142 UNP P00740 FA9_HUMAN 133 188 DBREF 3LC3 C 16 245 UNP P00740 FA9_HUMAN 227 461 DBREF 3LC3 D 87 142 UNP P00740 FA9_HUMAN 133 188 SEQADV 3LC3 MET B 86 UNP P00740 INITIATING METHIONINE SEQADV 3LC3 MET D 86 UNP P00740 INITIATING METHIONINE SEQRES 1 A 235 VAL VAL GLY GLY GLU ASP ALA LYS PRO GLY GLN PHE PRO SEQRES 2 A 235 TRP GLN VAL VAL LEU ASN GLY LYS VAL ASP ALA PHE CYS SEQRES 3 A 235 GLY GLY SER ILE VAL ASN GLU LYS TRP ILE VAL THR ALA SEQRES 4 A 235 ALA HIS CYS VAL GLU THR GLY VAL LYS ILE THR VAL VAL SEQRES 5 A 235 ALA GLY GLU HIS ASN ILE GLU GLU THR GLU HIS THR GLU SEQRES 6 A 235 GLN LYS ARG ASN VAL ILE ARG ILE ILE PRO HIS HIS ASN SEQRES 7 A 235 TYR ASN ALA ALA ILE ASN LYS TYR ASN HIS ASP ILE ALA SEQRES 8 A 235 LEU LEU GLU LEU ASP GLU PRO LEU VAL LEU ASN SER TYR SEQRES 9 A 235 VAL THR PRO ILE CYS ILE ALA ASP LYS GLU TYR THR ASN SEQRES 10 A 235 ILE PHE LEU LYS PHE GLY SER GLY TYR VAL SER GLY TRP SEQRES 11 A 235 GLY ARG VAL PHE HIS LYS GLY ARG SER ALA LEU VAL LEU SEQRES 12 A 235 GLN TYR LEU ARG VAL PRO LEU VAL ASP ARG ALA THR CYS SEQRES 13 A 235 LEU ARG SER THR LYS PHE THR ILE TYR ASN ASN MET PHE SEQRES 14 A 235 CYS ALA GLY PHE HIS GLU GLY GLY ARG ASP SER CYS GLN SEQRES 15 A 235 GLY ASP SER GLY GLY PRO HIS VAL THR GLU VAL GLU GLY SEQRES 16 A 235 THR SER PHE LEU THR GLY ILE ILE SER TRP GLY GLU GLU SEQRES 17 A 235 CYS ALA MET LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 A 235 SER ARG TYR VAL ASN TRP ILE LYS GLU LYS THR LYS LEU SEQRES 19 A 235 THR SEQRES 1 B 57 MET THR CYS ASN ILE LYS ASN GLY ARG CYS GLU GLN PHE SEQRES 2 B 57 CYS LYS ASN SER ALA ASP ASN LYS VAL VAL CYS SER CYS SEQRES 3 B 57 THR GLU GLY TYR ARG LEU ALA GLU ASN GLN LYS SER CYS SEQRES 4 B 57 GLU PRO ALA VAL PRO PHE PRO CYS GLY ARG VAL SER VAL SEQRES 5 B 57 SER GLN THR SER LYS SEQRES 1 C 235 VAL VAL GLY GLY GLU ASP ALA LYS PRO GLY GLN PHE PRO SEQRES 2 C 235 TRP GLN VAL VAL LEU ASN GLY LYS VAL ASP ALA PHE CYS SEQRES 3 C 235 GLY GLY SER ILE VAL ASN GLU LYS TRP ILE VAL THR ALA SEQRES 4 C 235 ALA HIS CYS VAL GLU THR GLY VAL LYS ILE THR VAL VAL SEQRES 5 C 235 ALA GLY GLU HIS ASN ILE GLU GLU THR GLU HIS THR GLU SEQRES 6 C 235 GLN LYS ARG ASN VAL ILE ARG ILE ILE PRO HIS HIS ASN SEQRES 7 C 235 TYR ASN ALA ALA ILE ASN LYS TYR ASN HIS ASP ILE ALA SEQRES 8 C 235 LEU LEU GLU LEU ASP GLU PRO LEU VAL LEU ASN SER TYR SEQRES 9 C 235 VAL THR PRO ILE CYS ILE ALA ASP LYS GLU TYR THR ASN SEQRES 10 C 235 ILE PHE LEU LYS PHE GLY SER GLY TYR VAL SER GLY TRP SEQRES 11 C 235 GLY ARG VAL PHE HIS LYS GLY ARG SER ALA LEU VAL LEU SEQRES 12 C 235 GLN TYR LEU ARG VAL PRO LEU VAL ASP ARG ALA THR CYS SEQRES 13 C 235 LEU ARG SER THR LYS PHE THR ILE TYR ASN ASN MET PHE SEQRES 14 C 235 CYS ALA GLY PHE HIS GLU GLY GLY ARG ASP SER CYS GLN SEQRES 15 C 235 GLY ASP SER GLY GLY PRO HIS VAL THR GLU VAL GLU GLY SEQRES 16 C 235 THR SER PHE LEU THR GLY ILE ILE SER TRP GLY GLU GLU SEQRES 17 C 235 CYS ALA MET LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 C 235 SER ARG TYR VAL ASN TRP ILE LYS GLU LYS THR LYS LEU SEQRES 19 C 235 THR SEQRES 1 D 57 MET THR CYS ASN ILE LYS ASN GLY ARG CYS GLU GLN PHE SEQRES 2 D 57 CYS LYS ASN SER ALA ASP ASN LYS VAL VAL CYS SER CYS SEQRES 3 D 57 THR GLU GLY TYR ARG LEU ALA GLU ASN GLN LYS SER CYS SEQRES 4 D 57 GLU PRO ALA VAL PRO PHE PRO CYS GLY ARG VAL SER VAL SEQRES 5 D 57 SER GLN THR SER LYS HET IYX A 1 22 HET IYX A 2 22 HET CA A 246 1 HET IYX C 1 22 HET IYX C 2 22 HET CA C 246 1 HETNAM IYX 1-[5-(3,4-DIMETHOXYPHENYL)-1-BENZOTHIOPHEN-2- HETNAM 2 IYX YL]METHANEDIAMINE HETNAM CA CALCIUM ION FORMUL 5 IYX 4(C17 H18 N2 O2 S) FORMUL 7 CA 2(CA 2+) FORMUL 11 HOH *420(H2 O) HELIX 1 1 ALA A 55 VAL A 59 5 5 HELIX 2 2 ASP A 125 PHE A 133 1 11 HELIX 3 3 ASP A 164 SER A 171 1 8 HELIX 4 4 TYR A 234 THR A 242 1 9 HELIX 5 5 ILE B 90 CYS B 95 5 6 HELIX 6 6 ALA C 55 VAL C 59 5 5 HELIX 7 7 ASP C 125 PHE C 133 1 11 HELIX 8 8 ASP C 164 SER C 171 1 8 HELIX 9 9 TYR C 234 THR C 242 1 9 HELIX 10 10 ILE D 90 CYS D 95 5 6 SHEET 1 A 8 GLU A 20 ASP A 21 0 SHEET 2 A 8 GLN A 156 VAL A 163 -1 O TYR A 157 N GLU A 20 SHEET 3 A 8 MET A 180 ALA A 183 -1 O CYS A 182 N VAL A 163 SHEET 4 A 8 GLY A 226 LYS A 230 -1 O TYR A 228 N PHE A 181 SHEET 5 A 8 THR A 206 TRP A 215 -1 N TRP A 215 O ILE A 227 SHEET 6 A 8 PRO A 198 VAL A 203 -1 N VAL A 203 O THR A 206 SHEET 7 A 8 SER A 135 GLY A 140 -1 N TYR A 137 O VAL A 200 SHEET 8 A 8 GLN A 156 VAL A 163 -1 O VAL A 160 N GLY A 136 SHEET 1 B 7 GLN A 30 ASN A 34 0 SHEET 2 B 7 CYS A 42 ASN A 48 -1 O CYS A 42 N LEU A 33 SHEET 3 B 7 TRP A 51 THR A 54 -1 O VAL A 53 N SER A 45 SHEET 4 B 7 ALA A 104 LEU A 108 -1 O LEU A 106 N ILE A 52 SHEET 5 B 7 GLN A 81 PRO A 90 -1 N ARG A 87 O GLU A 107 SHEET 6 B 7 THR A 65 ALA A 68 -1 N ALA A 68 O GLN A 81 SHEET 7 B 7 GLN A 30 ASN A 34 -1 N ASN A 34 O THR A 65 SHEET 1 C 2 PHE B 98 LYS B 100 0 SHEET 2 C 2 VAL B 108 SER B 110 -1 O SER B 110 N PHE B 98 SHEET 1 D 2 TYR B 115 LEU B 117 0 SHEET 2 D 2 CYS B 124 PRO B 126 -1 O GLU B 125 N ARG B 116 SHEET 1 E 8 GLU C 20 ASP C 21 0 SHEET 2 E 8 GLN C 156 VAL C 163 -1 O TYR C 157 N GLU C 20 SHEET 3 E 8 MET C 180 ALA C 183 -1 O CYS C 182 N VAL C 163 SHEET 4 E 8 GLY C 226 LYS C 230 -1 O TYR C 228 N PHE C 181 SHEET 5 E 8 THR C 206 TRP C 215 -1 N TRP C 215 O ILE C 227 SHEET 6 E 8 PRO C 198 VAL C 203 -1 N VAL C 203 O THR C 206 SHEET 7 E 8 SER C 135 GLY C 140 -1 N TYR C 137 O VAL C 200 SHEET 8 E 8 GLN C 156 VAL C 163 -1 O VAL C 160 N GLY C 136 SHEET 1 F 7 GLN C 30 ASN C 34 0 SHEET 2 F 7 CYS C 42 ASN C 48 -1 O CYS C 42 N LEU C 33 SHEET 3 F 7 TRP C 51 THR C 54 -1 O TRP C 51 N VAL C 47 SHEET 4 F 7 ALA C 104 LEU C 108 -1 O ALA C 104 N THR C 54 SHEET 5 F 7 GLN C 81 PRO C 90 -1 N ILE C 89 O LEU C 105 SHEET 6 F 7 THR C 65 ALA C 68 -1 N VAL C 66 O ARG C 83 SHEET 7 F 7 GLN C 30 ASN C 34 -1 N ASN C 34 O THR C 65 SHEET 1 G 2 PHE D 98 LYS D 100 0 SHEET 2 G 2 VAL D 108 SER D 110 -1 O SER D 110 N PHE D 98 SHEET 1 H 2 TYR D 115 LEU D 117 0 SHEET 2 H 2 CYS D 124 PRO D 126 -1 O GLU D 125 N ARG D 116 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.05 SSBOND 2 CYS A 122 CYS B 132 1555 1555 2.06 SSBOND 3 CYS A 168 CYS A 182 1555 1555 1.94 SSBOND 4 CYS A 191 CYS A 220 1555 1555 2.05 SSBOND 5 CYS B 88 CYS B 99 1555 1555 2.03 SSBOND 6 CYS B 95 CYS B 109 1555 1555 2.03 SSBOND 7 CYS B 111 CYS B 124 1555 1555 2.06 SSBOND 8 CYS C 42 CYS C 58 1555 1555 2.02 SSBOND 9 CYS C 122 CYS D 132 1555 1555 2.04 SSBOND 10 CYS C 168 CYS C 182 1555 1555 1.95 SSBOND 11 CYS C 191 CYS C 220 1555 1555 2.07 SSBOND 12 CYS D 88 CYS D 99 1555 1555 2.02 SSBOND 13 CYS D 95 CYS D 109 1555 1555 2.05 SSBOND 14 CYS D 111 CYS D 124 1555 1555 2.06 LINK O GLU A 75 CA CA A 246 1555 1555 2.27 LINK O ASN C 72 CA CA C 246 1555 1555 2.28 LINK O GLU C 75 CA CA C 246 1555 1555 2.30 LINK OE1 GLU C 70 CA CA C 246 1555 1555 2.30 LINK OE2 GLU C 80 CA CA C 246 1555 1555 2.32 LINK O ASN A 72 CA CA A 246 1555 1555 2.33 LINK OE1 GLU A 70 CA CA A 246 1555 1555 2.33 LINK OE2 GLU A 80 CA CA A 246 1555 1555 2.39 LINK OE1 GLU C 77 CA CA C 246 1555 1555 2.43 LINK OE1 GLU A 77 CA CA A 246 1555 1555 2.45 LINK OE2 GLU C 77 CA CA C 246 1555 1555 2.60 LINK OE2 GLU A 77 CA CA A 246 1555 1555 2.74 LINK CA CA A 246 O HOH A 6 1555 1555 2.34 LINK CA CA C 246 O HOH C 400 1555 1555 2.38 SITE 1 AC1 12 IYX A 2 TYR A 99 ASP A 189 SER A 190 SITE 2 AC1 12 CYS A 191 GLN A 192 SER A 195 GLY A 216 SITE 3 AC1 12 GLU A 217 CYS A 220 GLY A 226 HOH A 351 SITE 1 AC2 11 IYX A 1 ASN A 97 LYS A 98 TYR A 99 SITE 2 AC2 11 HIS A 147 PHE A 174 TRP A 215 GLY A 216 SITE 3 AC2 11 GLU A 217 GLU A 219 HOH C 346 SITE 1 AC3 6 HOH A 6 GLU A 70 ASN A 72 GLU A 75 SITE 2 AC3 6 GLU A 77 GLU A 80 SITE 1 AC4 10 IYX C 2 TYR C 99 ASP C 189 SER C 190 SITE 2 AC4 10 GLN C 192 SER C 195 GLY C 216 GLU C 217 SITE 3 AC4 10 CYS C 220 GLY C 226 SITE 1 AC5 13 IYX C 1 ASN C 97 LYS C 98 TYR C 99 SITE 2 AC5 13 HIS C 147 PHE C 174 TRP C 215 GLY C 216 SITE 3 AC5 13 GLU C 217 GLU C 219 HOH C 344 HOH C 405 SITE 4 AC5 13 HOH C 420 SITE 1 AC6 6 GLU C 70 ASN C 72 GLU C 75 GLU C 77 SITE 2 AC6 6 GLU C 80 HOH C 400 CRYST1 66.922 96.035 44.391 90.00 89.93 90.00 P 1 21 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 0.014943 -0.000014 -0.000019 0.00000 SCALE2 0.000000 0.010413 0.000007 0.00000 SCALE3 0.000000 0.000000 0.022527 0.00000