HEADER OXIDOREDUCTASE 30-NOV-09 3KW4 TITLE CRYSTAL STRUCTURE OF CYTOCHROME 2B4 IN COMPLEX WITH THE ANTI-PLATELET TITLE 2 DRUG TICLOPIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 2B4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYPIIB4, P450-LM2, ISOZYME 2, P450 TYPES B0 AND B1; COMPND 5 EC: 1.14.14.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: CYP2B4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOPP3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKK KEYWDS P450, CYTOCHROME P450 2B4, MONOOXYGENASE, OXIDOREDUCTASE, MEMBRANE KEYWDS 2 PROTEIN, CYP 2B4, CYP LM2, ENDOPLASMIC RETICULUM, HEME, IRON, KEYWDS 3 MEMBRANE, METAL-BINDING, MICROSOME EXPDTA X-RAY DIFFRACTION AUTHOR S.C.GAY,K.MAEKAWA,A.G.ROBERTS,W.-X.HONG,Q.ZHANG,C.D.STOUT,J.R.HALPERT REVDAT 5 06-SEP-23 3KW4 1 REMARK REVDAT 4 13-OCT-21 3KW4 1 REMARK SEQADV REVDAT 3 31-AUG-11 3KW4 1 HETATM VERSN REVDAT 2 16-FEB-11 3KW4 1 JRNL REVDAT 1 15-SEP-10 3KW4 0 JRNL AUTH S.C.GAY,A.G.ROBERTS,K.MAEKAWA,J.C.TALAKAD,W.X.HONG,Q.ZHANG, JRNL AUTH 2 C.D.STOUT,J.R.HALPERT JRNL TITL STRUCTURES OF CYTOCHROME P450 2B4 COMPLEXED WITH THE JRNL TITL 2 ANTIPLATELET DRUGS TICLOPIDINE AND CLOPIDOGREL. JRNL REF BIOCHEMISTRY V. 49 8709 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20815363 JRNL DOI 10.1021/BI100914Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.ZHAO,M.A.WHITE,B.K.MURALIDHARA,L.SUN,J.R.HALPERT,C.D.STOUT REMARK 1 TITL STRUCTURE OF MICROSOMAL CYTOCHROME P450 2B4 COMPLEXED WITH REMARK 1 TITL 2 THE ANTIFUNGAL DRUG BIFONAZOLE: INSIGHT INTO P450 REMARK 1 TITL 3 CONFORMATIONAL PLASTICITY AND MEMBRANE INTERACTION. REMARK 1 REF J.BIOL.CHEM. V. 281 5973 2006 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 16373351 REMARK 1 DOI 10.1074/JBC.M511464200 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.E.SCOTT,M.A.WHITE,Y.A.HE,E.F.JOHNSON,C.D.STOUT,J.R.HALPERT REMARK 1 TITL STRUCTURE OF MAMMALIAN CYTOCHROME P450 2B4 COMPLEXED WITH REMARK 1 TITL 2 4-(4-CHLOROPHENYL)IMIDAZOLE AT 1.9 {ANGSTROM} RESOLUTION: REMARK 1 TITL 3 INSIGHT INTO THE RANGE OF P450 CONFORMATIONS AND REMARK 1 TITL 4 COORDINATION OF REDOX PARTNER BINDING. REMARK 1 REF J.BIOL.CHEM. V. 279 27294 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15100217 REMARK 1 DOI 10.1074/JBC.M403349200 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.E.SCOTT,Y.A.HE,M.R.WESTER,M.A.WHITE,C.C.CHIN,J.R.HALPERT, REMARK 1 AUTH 2 E.F.JOHNSON,C.D.STOUT REMARK 1 TITL AN OPEN CONFORMATION OF MAMMALIAN CYTOCHROME P450 2B4 AT 1.6 REMARK 1 TITL 2 A RESOLUTION. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 13196 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 14563924 REMARK 1 DOI 10.1073/PNAS.2133986100 REMARK 1 REFERENCE 4 REMARK 1 AUTH Y.ZHAO,L.SUN,B.K.MURALIDHARA,M.A.WHITE,C.D.STOUT,J.R.HALPERT REMARK 1 TITL STRUCTURAL AND THERMODYNAMIC CONSEQUENCES OF REMARK 1 TITL 2 1-(4-CHLOROPHENYL)IMIDAZOLE BINDING TO CYTOCHROME P450 2B4. REMARK 1 REF BIOCHEMISTRY V. 46 11559 2007 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 17887776 REMARK 1 DOI 10.1021/BI7011614 REMARK 1 REFERENCE 5 REMARK 1 AUTH S.C.GAY,L.SUN,K.MAEKAWA,J.R.HALPERT,C.D.STOUT REMARK 1 TITL CRYSTAL STRUCTURES OF CYTOCHROME P450 2B4 IN COMPLEX WITH REMARK 1 TITL 2 THE INHIBITOR 1-BIPHENYL-4-METHYL-1H-IMIDAZOLE: REMARK 1 TITL 3 LIGAND-INDUCED STRUCTURAL RESPONSE THROUGH ALPHA-HELICAL REMARK 1 TITL 4 REPOSITIONING REMARK 1 REF BIOCHEMISTRY V. 48 4762 2009 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 19397311 REMARK 1 DOI 10.1021/BI9003765 REMARK 2 REMARK 2 RESOLUTION. 2.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19135 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1028 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) : 2.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1387 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3730 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3693 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 208 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.73500 REMARK 3 B22 (A**2) : -5.73500 REMARK 3 B33 (A**2) : 11.47000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.626 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.330 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.253 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.152 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3993 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5438 ; 1.406 ; 2.049 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 465 ; 5.844 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;33.840 ;22.644 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 627 ;18.074 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;22.894 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 622 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2983 ; 0.011 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2326 ; 0.897 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3767 ; 1.736 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1667 ; 2.554 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1671 ; 4.317 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3KW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000056520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.670 REMARK 200 RESOLUTION RANGE LOW (A) : 80.973 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : 0.10100 REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : 0.41600 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.3 REMARK 200 STARTING MODEL: PDB ENTRY 1SUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8000, 0.2 M MGCL2 AND REMARK 280 0.1 M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 91.38000 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 45.69000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.69000 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 91.38000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 MET A 20 REMARK 465 ALA A 21 REMARK 465 LYS A 22 REMARK 465 LYS A 23 REMARK 465 THR A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 HIS A 493 REMARK 465 HIS A 494 REMARK 465 HIS A 495 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 LYS A 27 CG CD CE NZ REMARK 470 ARG A 48 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 119 CG CD OE1 OE2 REMARK 470 MET A 137 CG SD CE REMARK 470 ASP A 275 CG OD1 OD2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 GLN A 330 CG CD OE1 NE2 REMARK 470 HIS A 335 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 422 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 473 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 492 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 29 166.66 89.20 REMARK 500 VAL A 39 -65.01 78.85 REMARK 500 ALA A 92 -49.42 -26.18 REMARK 500 GLN A 109 19.89 51.33 REMARK 500 LEU A 129 -76.26 -66.19 REMARK 500 ALA A 130 -58.06 -22.78 REMARK 500 ASP A 134 -62.75 -154.22 REMARK 500 PHE A 135 -35.32 71.94 REMARK 500 LYS A 161 40.72 34.75 REMARK 500 ASP A 192 109.49 -57.61 REMARK 500 PRO A 258 2.12 -56.21 REMARK 500 PRO A 279 29.51 -69.44 REMARK 500 THR A 300 -55.61 -123.32 REMARK 500 HIS A 335 -89.32 -65.99 REMARK 500 ARG A 378 38.01 37.68 REMARK 500 ASN A 409 87.63 -173.22 REMARK 500 SER A 430 -164.50 70.19 REMARK 500 VAL A 477 -5.48 -56.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CH0 A 603 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 CH0 A 603 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 HEM A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 436 SG REMARK 620 2 HEM A 500 NA 103.8 REMARK 620 3 HEM A 500 NB 85.7 96.2 REMARK 620 4 HEM A 500 NC 82.3 173.9 84.1 REMARK 620 5 HEM A 500 ND 99.4 84.0 174.6 95.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TIC A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM5 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM5 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CH0 A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PO5 RELATED DB: PDB REMARK 900 LIGAND FREE STRUCTURE OF 2B4 REMARK 900 RELATED ID: 1SUO RELATED DB: PDB REMARK 900 2B4 IN COMPLEX WITH 4-(4-CHLOROPHENYL)IMIDAZOLE REMARK 900 RELATED ID: 2BDM RELATED DB: PDB REMARK 900 2B4 IN COMPLEX WITH BIFONAZOLE REMARK 900 RELATED ID: 2Q6N RELATED DB: PDB REMARK 900 2B4 IN COMPLEX WITH 4-(4-CHLOROPHENYL)IMIDAZOLE REMARK 900 RELATED ID: 3G93 RELATED DB: PDB REMARK 900 SINGLE LIGAND OCCUPANCY STRUCTURE OF 2B4 IN COMPLEX WITH 1-BIPHENYL- REMARK 900 4-METHYL-1H-IMIDAZOLE REMARK 900 RELATED ID: 3G5N RELATED DB: PDB REMARK 900 TRIPLE LIGAND OCCUPANCY STRUCTURE OF 2B4 IN COMPLEX WITH 1-BIPHENYL- REMARK 900 4-METHYL-1H-IMIDAZOLE REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS INDICATE THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE REMARK 999 REFERENCE AT RESIDUE 221 DBREF 3KW4 A 20 491 UNP P00178 CP2B4_RABIT 1 491 SEQADV 3KW4 ALA A 21 UNP P00178 GLU 2 ENGINEERED MUTATION SEQADV 3KW4 A UNP P00178 PHE 3 DELETION SEQADV 3KW4 A UNP P00178 SER 4 DELETION SEQADV 3KW4 A UNP P00178 LEU 5 DELETION SEQADV 3KW4 A UNP P00178 LEU 6 DELETION SEQADV 3KW4 A UNP P00178 LEU 7 DELETION SEQADV 3KW4 A UNP P00178 LEU 8 DELETION SEQADV 3KW4 A UNP P00178 LEU 9 DELETION SEQADV 3KW4 A UNP P00178 ALA 10 DELETION SEQADV 3KW4 A UNP P00178 PHE 11 DELETION SEQADV 3KW4 A UNP P00178 LEU 12 DELETION SEQADV 3KW4 A UNP P00178 ALA 13 DELETION SEQADV 3KW4 A UNP P00178 GLY 14 DELETION SEQADV 3KW4 A UNP P00178 LEU 15 DELETION SEQADV 3KW4 A UNP P00178 LEU 16 DELETION SEQADV 3KW4 A UNP P00178 LEU 17 DELETION SEQADV 3KW4 A UNP P00178 LEU 18 DELETION SEQADV 3KW4 A UNP P00178 LEU 19 DELETION SEQADV 3KW4 A UNP P00178 PHE 20 DELETION SEQADV 3KW4 A UNP P00178 ARG 21 DELETION SEQADV 3KW4 LYS A 22 UNP P00178 GLY 22 ENGINEERED MUTATION SEQADV 3KW4 LYS A 23 UNP P00178 HIS 23 ENGINEERED MUTATION SEQADV 3KW4 THR A 24 UNP P00178 PRO 24 ENGINEERED MUTATION SEQADV 3KW4 SER A 25 UNP P00178 LYS 25 ENGINEERED MUTATION SEQADV 3KW4 SER A 26 UNP P00178 ALA 26 ENGINEERED MUTATION SEQADV 3KW4 LYS A 27 UNP P00178 HIS 27 ENGINEERED MUTATION SEQADV 3KW4 LYS A 29 UNP P00178 ARG 29 ENGINEERED MUTATION SEQADV 3KW4 SER A 221 UNP P00178 PRO 221 SEE REMARK 999 SEQADV 3KW4 TYR A 226 UNP P00178 HIS 226 ENGINEERED MUTATION SEQADV 3KW4 HIS A 492 UNP P00178 EXPRESSION TAG SEQADV 3KW4 HIS A 493 UNP P00178 EXPRESSION TAG SEQADV 3KW4 HIS A 494 UNP P00178 EXPRESSION TAG SEQADV 3KW4 HIS A 495 UNP P00178 EXPRESSION TAG SEQRES 1 A 476 MET ALA LYS LYS THR SER SER LYS GLY LYS LEU PRO PRO SEQRES 2 A 476 GLY PRO SER PRO LEU PRO VAL LEU GLY ASN LEU LEU GLN SEQRES 3 A 476 MET ASP ARG LYS GLY LEU LEU ARG SER PHE LEU ARG LEU SEQRES 4 A 476 ARG GLU LYS TYR GLY ASP VAL PHE THR VAL TYR LEU GLY SEQRES 5 A 476 SER ARG PRO VAL VAL VAL LEU CYS GLY THR ASP ALA ILE SEQRES 6 A 476 ARG GLU ALA LEU VAL ASP GLN ALA GLU ALA PHE SER GLY SEQRES 7 A 476 ARG GLY LYS ILE ALA VAL VAL ASP PRO ILE PHE GLN GLY SEQRES 8 A 476 TYR GLY VAL ILE PHE ALA ASN GLY GLU ARG TRP ARG ALA SEQRES 9 A 476 LEU ARG ARG PHE SER LEU ALA THR MET ARG ASP PHE GLY SEQRES 10 A 476 MET GLY LYS ARG SER VAL GLU GLU ARG ILE GLN GLU GLU SEQRES 11 A 476 ALA ARG CYS LEU VAL GLU GLU LEU ARG LYS SER LYS GLY SEQRES 12 A 476 ALA LEU LEU ASP ASN THR LEU LEU PHE HIS SER ILE THR SEQRES 13 A 476 SER ASN ILE ILE CYS SER ILE VAL PHE GLY LYS ARG PHE SEQRES 14 A 476 ASP TYR LYS ASP PRO VAL PHE LEU ARG LEU LEU ASP LEU SEQRES 15 A 476 PHE PHE GLN SER PHE SER LEU ILE SER SER PHE SER SER SEQRES 16 A 476 GLN VAL PHE GLU LEU PHE SER GLY PHE LEU LYS TYR PHE SEQRES 17 A 476 PRO GLY THR HIS ARG GLN ILE TYR ARG ASN LEU GLN GLU SEQRES 18 A 476 ILE ASN THR PHE ILE GLY GLN SER VAL GLU LYS HIS ARG SEQRES 19 A 476 ALA THR LEU ASP PRO SER ASN PRO ARG ASP PHE ILE ASP SEQRES 20 A 476 VAL TYR LEU LEU ARG MET GLU LYS ASP LYS SER ASP PRO SEQRES 21 A 476 SER SER GLU PHE HIS HIS GLN ASN LEU ILE LEU THR VAL SEQRES 22 A 476 LEU SER LEU PHE PHE ALA GLY THR GLU THR THR SER THR SEQRES 23 A 476 THR LEU ARG TYR GLY PHE LEU LEU MET LEU LYS TYR PRO SEQRES 24 A 476 HIS VAL THR GLU ARG VAL GLN LYS GLU ILE GLU GLN VAL SEQRES 25 A 476 ILE GLY SER HIS ARG PRO PRO ALA LEU ASP ASP ARG ALA SEQRES 26 A 476 LYS MET PRO TYR THR ASP ALA VAL ILE HIS GLU ILE GLN SEQRES 27 A 476 ARG LEU GLY ASP LEU ILE PRO PHE GLY VAL PRO HIS THR SEQRES 28 A 476 VAL THR LYS ASP THR GLN PHE ARG GLY TYR VAL ILE PRO SEQRES 29 A 476 LYS ASN THR GLU VAL PHE PRO VAL LEU SER SER ALA LEU SEQRES 30 A 476 HIS ASP PRO ARG TYR PHE GLU THR PRO ASN THR PHE ASN SEQRES 31 A 476 PRO GLY HIS PHE LEU ASP ALA ASN GLY ALA LEU LYS ARG SEQRES 32 A 476 ASN GLU GLY PHE MET PRO PHE SER LEU GLY LYS ARG ILE SEQRES 33 A 476 CYS LEU GLY GLU GLY ILE ALA ARG THR GLU LEU PHE LEU SEQRES 34 A 476 PHE PHE THR THR ILE LEU GLN ASN PHE SER ILE ALA SER SEQRES 35 A 476 PRO VAL PRO PRO GLU ASP ILE ASP LEU THR PRO ARG GLU SEQRES 36 A 476 SER GLY VAL GLY ASN VAL PRO PRO SER TYR GLN ILE ARG SEQRES 37 A 476 PHE LEU ALA ARG HIS HIS HIS HIS HET HEM A 500 43 HET TIC A 600 34 HET CM5 A 601 34 HET CM5 A 602 34 HET CH0 A 603 80 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM TIC TICLOPIDINE HETNAM CM5 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE HETNAM CH0 2-{[(3ALPHA,5ALPHA,7ALPHA,8ALPHA,10ALPHA,12ALPHA, HETNAM 2 CH0 17ALPHA)-3,12-BIS{2-[(4-O-ALPHA-D-GLUCOPYRANOSYL-BETA- HETNAM 3 CH0 D-GLUCOPYRANOSYL)OXY]ETHOXY}CHOLAN-7-YL]OXY}ETHYL 4-O- HETNAM 4 CH0 ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE HETSYN HEM HEME HETSYN TIC 5-(2-CHLOROBENZYL)-4,5,6,7-TETRAHYDROTHIENO[3,2- HETSYN 2 TIC C]PYRIDINE HETSYN CM5 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D- HETSYN 2 CM5 GLUCOPYRANOSIDE; CYMAL-5 HETSYN CH0 3,7,12-TRIS[(-D-MALTOPYRANOSYL)ETHYLOXY]CHOLANE FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 TIC C14 H14 CL N S FORMUL 4 CM5 2(C23 H42 O11) FORMUL 6 CH0 C66 H114 O36 FORMUL 7 HOH *31(H2 O) HELIX 1 1 ASN A 42 MET A 46 5 5 HELIX 2 2 GLY A 50 GLY A 63 1 14 HELIX 3 3 GLY A 80 VAL A 89 1 10 HELIX 4 4 ILE A 101 VAL A 103 5 3 HELIX 5 5 VAL A 104 GLN A 109 1 6 HELIX 6 6 TYR A 111 ALA A 116 1 6 HELIX 7 7 ASN A 117 ASP A 134 1 18 HELIX 8 8 SER A 141 SER A 160 1 20 HELIX 9 9 ASN A 167 PHE A 184 1 18 HELIX 10 10 ASP A 192 SER A 210 1 19 HELIX 11 11 SER A 211 LYS A 225 1 15 HELIX 12 12 GLY A 229 THR A 255 1 27 HELIX 13 13 ASP A 263 ASP A 275 1 13 HELIX 14 14 LYS A 276 ASP A 278 5 3 HELIX 15 15 HIS A 284 THR A 300 1 17 HELIX 16 16 THR A 300 TYR A 317 1 18 HELIX 17 17 TYR A 317 ILE A 332 1 16 HELIX 18 18 ALA A 339 LYS A 345 5 7 HELIX 19 19 MET A 346 ASP A 361 1 16 HELIX 20 20 VAL A 391 HIS A 397 1 7 HELIX 21 21 ASN A 409 LEU A 414 5 6 HELIX 22 22 GLY A 438 PHE A 457 1 20 HELIX 23 23 PRO A 464 ILE A 468 5 5 SHEET 1 A 5 VAL A 65 LEU A 70 0 SHEET 2 A 5 ARG A 73 LEU A 78 -1 O VAL A 77 N PHE A 66 SHEET 3 A 5 GLU A 387 PRO A 390 1 O GLU A 387 N VAL A 76 SHEET 4 A 5 HIS A 369 THR A 370 -1 N HIS A 369 O VAL A 388 SHEET 5 A 5 GLY A 97 ARG A 98 -1 N GLY A 97 O THR A 370 SHEET 1 B 2 THR A 375 PHE A 377 0 SHEET 2 B 2 TYR A 380 ILE A 382 -1 O TYR A 380 N PHE A 377 SHEET 1 C 2 SER A 458 ALA A 460 0 SHEET 2 C 2 ARG A 487 LEU A 489 -1 O ARG A 487 N ALA A 460 SHEET 1 D 2 GLU A 474 SER A 475 0 SHEET 2 D 2 ASN A 479 VAL A 480 -1 O VAL A 480 N GLU A 474 LINK SG CYS A 436 FE HEM A 500 1555 1555 2.40 SITE 1 AC1 19 ARG A 98 ILE A 114 TRP A 121 ARG A 125 SITE 2 AC1 19 ALA A 298 GLY A 299 THR A 302 THR A 303 SITE 3 AC1 19 THR A 306 ILE A 363 HIS A 369 PRO A 428 SITE 4 AC1 19 PHE A 429 SER A 430 ARG A 434 CYS A 436 SITE 5 AC1 19 LEU A 437 GLY A 438 TIC A 600 SITE 1 AC2 11 ILE A 114 PHE A 206 ILE A 209 SER A 210 SITE 2 AC2 11 PHE A 297 ALA A 298 GLU A 301 THR A 302 SITE 3 AC2 11 VAL A 367 GLY A 478 HEM A 500 SITE 1 AC3 7 LEU A 43 MET A 46 ASP A 47 LEU A 219 SITE 2 AC3 7 TYR A 226 PHE A 227 HOH A1028 SITE 1 AC4 9 LYS A 186 PHE A 188 PHE A 195 LEU A 198 SITE 2 AC4 9 PHE A 202 ILE A 241 PHE A 244 LYS A 251 SITE 3 AC4 9 PHE A 296 SITE 1 AC5 3 PHE A 212 PHE A 227 GLU A 474 CRYST1 93.500 93.500 137.070 90.00 90.00 120.00 P 32 2 1 6 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 0.010695 0.006175 0.000000 0.00000 SCALE2 0.000000 0.012350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007296 0.00000