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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END