HEADER OXIDOREDUCTASE 02-AUG-06 2J0D TITLE CRYSTAL STRUCTURE OF HUMAN P450 3A4 IN COMPLEX WITH ERYTHROMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 3A4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SOLUBLE DOMAIN, RESIDUES 24-502; COMPND 5 SYNONYM: QUININE 3-MONOOXYGENASE, CYPIIIA4, NIFEDIPINE OXIDASE, COMPND 6 TAUROCHENODEOXYCHOLATE 6-ALPHA-HYDROXYLASE, NF-25, P450-PCN1; COMPND 7 EC: 1.14.14.1, 1.14.13.67, 1.14.13.97; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XL1 BLUE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PCWORI KEYWDS POLYMORPHISM, ERYTHROMYCIN, MONOOXYGENASE, METAL-BINDING, KEYWDS 2 TRANSMEMBRANE, OXIDOREDUCTASE, ENDOPLASMIC RETICULUM, DRUG KEYWDS 3 METABOLIZING ENZYME, P450, NADP, IRON, HEME, CYP3A4, MEMBRANE, KEYWDS 4 MICROSOME EXPDTA X-RAY DIFFRACTION AUTHOR T.SJOGREN,M.EKROOS REVDAT 5 13-DEC-23 2J0D 1 LINK REVDAT 4 08-MAY-19 2J0D 1 REMARK REVDAT 3 24-FEB-09 2J0D 1 VERSN REVDAT 2 20-SEP-06 2J0D 1 JRNL REVDAT 1 04-SEP-06 2J0D 0 JRNL AUTH M.EKROOS,T.SJOGREN JRNL TITL STRUCTURAL BASIS FOR LIGAND PROMISCUITY IN CYTOCHROME P450 JRNL TITL 2 3A4 JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 13682 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16954191 JRNL DOI 10.1073/PNAS.0603236103 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 27971 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) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.315 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1483 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1916 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 137 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.455 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.331 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.723 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7462 ; 0.011 ; 0.023 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10123 ; 1.332 ; 2.031 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 881 ; 5.835 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 302 ;36.899 ;23.775 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1334 ;21.009 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;15.935 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1128 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5486 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3596 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5133 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 252 ; 0.225 ; 0.200 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): 49 ; 0.217 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.285 ; 0.200 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): 4581 ; 0.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7294 ; 0.965 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3230 ; 1.141 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2825 ; 1.839 ; 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 : BABINET MODEL WITH 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 2J0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029541. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9390 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30291 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 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 1W0E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP CRYSTALLISATION USING 1:1 REMARK 280 RATIO OF PROTEIN AT 20-27 MG/ML AGAINST 0.1 M HEPES PH 7-7.5, REMARK 280 0.2 M LITHIUM SULFATE,0.8-1.0 M LITHIUM CHLORIDE AND 30% PEG4000, REMARK 280 PH 7.50, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.62300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.62300 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.62700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 105.35300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.62700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 105.35300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.62300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.62700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 105.35300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.62300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.62700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 105.35300 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 23 REMARK 465 ALA A 24 REMARK 465 TYR A 25 REMARK 465 GLY A 26 REMARK 465 THR A 27 REMARK 465 HIS A 28 REMARK 465 LEU A 196 REMARK 465 ASN A 197 REMARK 465 ASP A 214 REMARK 465 PHE A 215 REMARK 465 LEU A 216 REMARK 465 ASP A 217 REMARK 465 PRO A 218 REMARK 465 LEU A 261 REMARK 465 GLU A 262 REMARK 465 ASP A 263 REMARK 465 THR A 264 REMARK 465 GLN A 265 REMARK 465 LYS A 266 REMARK 465 HIS A 267 REMARK 465 ARG A 268 REMARK 465 VAL A 269 REMARK 465 ASP A 270 REMARK 465 LYS A 282 REMARK 465 GLU A 283 REMARK 465 THR A 284 REMARK 465 GLU A 285 REMARK 465 SER A 286 REMARK 465 ASP A 497 REMARK 465 GLY A 498 REMARK 465 THR A 499 REMARK 465 VAL A 500 REMARK 465 SER A 501 REMARK 465 GLY A 502 REMARK 465 ALA A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 HIS A 506 REMARK 465 HIS A 507 REMARK 465 MET B 23 REMARK 465 ALA B 24 REMARK 465 TYR B 25 REMARK 465 LEU B 196 REMARK 465 ASN B 197 REMARK 465 LEU B 211 REMARK 465 ARG B 212 REMARK 465 PHE B 213 REMARK 465 ASP B 214 REMARK 465 PHE B 215 REMARK 465 LEU B 216 REMARK 465 ASP B 217 REMARK 465 LEU B 261 REMARK 465 GLU B 262 REMARK 465 ASP B 263 REMARK 465 THR B 264 REMARK 465 GLN B 265 REMARK 465 LYS B 266 REMARK 465 HIS B 267 REMARK 465 ARG B 268 REMARK 465 VAL B 269 REMARK 465 ASP B 270 REMARK 465 ASN B 280 REMARK 465 SER B 281 REMARK 465 LYS B 282 REMARK 465 GLU B 283 REMARK 465 THR B 284 REMARK 465 GLU B 285 REMARK 465 SER B 286 REMARK 465 ASP B 497 REMARK 465 GLY B 498 REMARK 465 THR B 499 REMARK 465 VAL B 500 REMARK 465 SER B 501 REMARK 465 GLY B 502 REMARK 465 ALA B 503 REMARK 465 HIS B 504 REMARK 465 HIS B 505 REMARK 465 HIS B 506 REMARK 465 HIS B 507 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 168 CG CD CE NZ REMARK 470 HIS A 287 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 168 CG CD CE NZ REMARK 470 HIS B 287 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 VAL A 71 136.87 -170.56 REMARK 500 THR A 85 -14.97 -147.26 REMARK 500 VAL A 95 -54.45 -128.86 REMARK 500 VAL A 101 -35.42 -134.42 REMARK 500 PHE A 102 63.08 -116.83 REMARK 500 ASP A 123 -140.21 47.94 REMARK 500 PRO A 199 92.22 -35.05 REMARK 500 ASP A 201 20.46 -154.18 REMARK 500 PRO A 202 -98.75 -100.19 REMARK 500 SER A 259 43.38 -71.98 REMARK 500 ALA A 289 -138.14 -103.66 REMARK 500 LEU A 290 106.95 172.98 REMARK 500 TYR A 307 -71.42 -63.62 REMARK 500 ASN A 341 83.54 54.46 REMARK 500 LEU A 351 13.51 -66.20 REMARK 500 MET A 353 64.05 -111.92 REMARK 500 GLU A 354 -78.22 -12.12 REMARK 500 MET A 371 -45.85 61.44 REMARK 500 PRO A 405 -9.10 -58.78 REMARK 500 CYS A 442 98.61 -69.70 REMARK 500 CYS A 468 -164.19 -100.21 REMARK 500 PHE B 46 -54.60 73.41 REMARK 500 VAL B 95 -62.44 -108.80 REMARK 500 PHE B 102 59.80 -115.40 REMARK 500 MET B 114 6.41 -65.27 REMARK 500 ASP B 123 -136.37 55.38 REMARK 500 THR B 166 4.02 -67.17 REMARK 500 PHE B 189 38.48 -147.65 REMARK 500 PRO B 199 86.82 -51.78 REMARK 500 ASP B 201 -34.20 -144.20 REMARK 500 PRO B 202 -98.98 -69.53 REMARK 500 LYS B 209 42.48 -92.33 REMARK 500 VAL B 240 0.19 -67.31 REMARK 500 SER B 291 170.75 -59.72 REMARK 500 MET B 371 -39.46 68.16 REMARK 500 ASP B 380 107.94 -47.85 REMARK 500 ASN B 384 56.93 20.39 REMARK 500 ASN B 426 8.60 -61.77 REMARK 500 PRO B 439 -14.15 -46.88 REMARK 500 ASN B 441 -174.70 -68.96 REMARK 500 CYS B 468 -155.02 -147.99 REMARK 500 LEU B 479 44.79 -88.30 REMARK 500 LYS B 487 108.48 74.08 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 HEM A1497 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 442 SG REMARK 620 2 HEM A1497 NA 83.6 REMARK 620 3 HEM A1497 NB 85.0 92.3 REMARK 620 4 HEM A1497 NC 99.5 176.3 86.0 REMARK 620 5 HEM A1497 ND 97.7 84.9 175.9 96.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B1497 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 442 SG REMARK 620 2 HEM B1497 NA 103.0 REMARK 620 3 HEM B1497 NB 94.0 94.1 REMARK 620 4 HEM B1497 NC 86.5 170.4 86.8 REMARK 620 5 HEM B1497 ND 92.0 92.3 170.0 85.6 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 ERY A1498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B1497 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TQN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 3A4 REMARK 900 RELATED ID: 1W0E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4 REMARK 900 RELATED ID: 1W0F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4 REMARK 900 RELATED ID: 1W0G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4 REMARK 900 RELATED ID: 2J0C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN P450 3A4 IN COMPLEX WITH KETOCONAZOLE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE CONFLICT CONFLICT HAS BEEN DESRCRIBED BY REMARK 999 GONZALEZ ET AL., DNA VOL: 7, PAGES 79-86, 1998 DBREF 2J0D A 23 24 PDB 2J0D 2J0D 23 24 DBREF 2J0D A 25 503 UNP P08684 CP3A4_HUMAN 24 502 DBREF 2J0D A 504 507 PDB 2J0D 2J0D 504 507 DBREF 2J0D B 23 24 PDB 2J0D 2J0D 23 24 DBREF 2J0D B 25 503 UNP P08684 CP3A4_HUMAN 24 502 DBREF 2J0D B 504 507 PDB 2J0D 2J0D 504 507 SEQADV 2J0D VAL A 392 UNP P08684 TRP 391 CONFLICT SEQADV 2J0D VAL B 392 UNP P08684 TRP 391 CONFLICT SEQRES 1 A 485 MET ALA TYR GLY THR HIS SER HIS GLY LEU PHE LYS LYS SEQRES 2 A 485 LEU GLY ILE PRO GLY PRO THR PRO LEU PRO PHE LEU GLY SEQRES 3 A 485 ASN ILE LEU SER TYR HIS LYS GLY PHE CYS MET PHE ASP SEQRES 4 A 485 MET GLU CYS HIS LYS LYS TYR GLY LYS VAL TRP GLY PHE SEQRES 5 A 485 TYR ASP GLY GLN GLN PRO VAL LEU ALA ILE THR ASP PRO SEQRES 6 A 485 ASP MET ILE LYS THR VAL LEU VAL LYS GLU CYS TYR SER SEQRES 7 A 485 VAL PHE THR ASN ARG ARG PRO PHE GLY PRO VAL GLY PHE SEQRES 8 A 485 MET LYS SER ALA ILE SER ILE ALA GLU ASP GLU GLU TRP SEQRES 9 A 485 LYS ARG LEU ARG SER LEU LEU SER PRO THR PHE THR SER SEQRES 10 A 485 GLY LYS LEU LYS GLU MET VAL PRO ILE ILE ALA GLN TYR SEQRES 11 A 485 GLY ASP VAL LEU VAL ARG ASN LEU ARG ARG GLU ALA GLU SEQRES 12 A 485 THR GLY LYS PRO VAL THR LEU LYS ASP VAL PHE GLY ALA SEQRES 13 A 485 TYR SER MET ASP VAL ILE THR SER THR SER PHE GLY VAL SEQRES 14 A 485 ASN ILE ASP SER LEU ASN ASN PRO GLN ASP PRO PHE VAL SEQRES 15 A 485 GLU ASN THR LYS LYS LEU LEU ARG PHE ASP PHE LEU ASP SEQRES 16 A 485 PRO PHE PHE LEU SER ILE THR VAL PHE PRO PHE LEU ILE SEQRES 17 A 485 PRO ILE LEU GLU VAL LEU ASN ILE CYS VAL PHE PRO ARG SEQRES 18 A 485 GLU VAL THR ASN PHE LEU ARG LYS SER VAL LYS ARG MET SEQRES 19 A 485 LYS GLU SER ARG LEU GLU ASP THR GLN LYS HIS ARG VAL SEQRES 20 A 485 ASP PHE LEU GLN LEU MET ILE ASP SER GLN ASN SER LYS SEQRES 21 A 485 GLU THR GLU SER HIS LYS ALA LEU SER ASP LEU GLU LEU SEQRES 22 A 485 VAL ALA GLN SER ILE ILE PHE ILE PHE ALA GLY TYR GLU SEQRES 23 A 485 THR THR SER SER VAL LEU SER PHE ILE MET TYR GLU LEU SEQRES 24 A 485 ALA THR HIS PRO ASP VAL GLN GLN LYS LEU GLN GLU GLU SEQRES 25 A 485 ILE ASP ALA VAL LEU PRO ASN LYS ALA PRO PRO THR TYR SEQRES 26 A 485 ASP THR VAL LEU GLN MET GLU TYR LEU ASP MET VAL VAL SEQRES 27 A 485 ASN GLU THR LEU ARG LEU PHE PRO ILE ALA MET ARG LEU SEQRES 28 A 485 GLU ARG VAL CYS LYS LYS ASP VAL GLU ILE ASN GLY MET SEQRES 29 A 485 PHE ILE PRO LYS GLY VAL VAL VAL MET ILE PRO SER TYR SEQRES 30 A 485 ALA LEU HIS ARG ASP PRO LYS TYR TRP THR GLU PRO GLU SEQRES 31 A 485 LYS PHE LEU PRO GLU ARG PHE SER LYS LYS ASN LYS ASP SEQRES 32 A 485 ASN ILE ASP PRO TYR ILE TYR THR PRO PHE GLY SER GLY SEQRES 33 A 485 PRO ARG ASN CYS ILE GLY MET ARG PHE ALA LEU MET ASN SEQRES 34 A 485 MET LYS LEU ALA LEU ILE ARG VAL LEU GLN ASN PHE SER SEQRES 35 A 485 PHE LYS PRO CYS LYS GLU THR GLN ILE PRO LEU LYS LEU SEQRES 36 A 485 SER LEU GLY GLY LEU LEU GLN PRO GLU LYS PRO VAL VAL SEQRES 37 A 485 LEU LYS VAL GLU SER ARG ASP GLY THR VAL SER GLY ALA SEQRES 38 A 485 HIS HIS HIS HIS SEQRES 1 B 485 MET ALA TYR GLY THR HIS SER HIS GLY LEU PHE LYS LYS SEQRES 2 B 485 LEU GLY ILE PRO GLY PRO THR PRO LEU PRO PHE LEU GLY SEQRES 3 B 485 ASN ILE LEU SER TYR HIS LYS GLY PHE CYS MET PHE ASP SEQRES 4 B 485 MET GLU CYS HIS LYS LYS TYR GLY LYS VAL TRP GLY PHE SEQRES 5 B 485 TYR ASP GLY GLN GLN PRO VAL LEU ALA ILE THR ASP PRO SEQRES 6 B 485 ASP MET ILE LYS THR VAL LEU VAL LYS GLU CYS TYR SER SEQRES 7 B 485 VAL PHE THR ASN ARG ARG PRO PHE GLY PRO VAL GLY PHE SEQRES 8 B 485 MET LYS SER ALA ILE SER ILE ALA GLU ASP GLU GLU TRP SEQRES 9 B 485 LYS ARG LEU ARG SER LEU LEU SER PRO THR PHE THR SER SEQRES 10 B 485 GLY LYS LEU LYS GLU MET VAL PRO ILE ILE ALA GLN TYR SEQRES 11 B 485 GLY ASP VAL LEU VAL ARG ASN LEU ARG ARG GLU ALA GLU SEQRES 12 B 485 THR GLY LYS PRO VAL THR LEU LYS ASP VAL PHE GLY ALA SEQRES 13 B 485 TYR SER MET ASP VAL ILE THR SER THR SER PHE GLY VAL SEQRES 14 B 485 ASN ILE ASP SER LEU ASN ASN PRO GLN ASP PRO PHE VAL SEQRES 15 B 485 GLU ASN THR LYS LYS LEU LEU ARG PHE ASP PHE LEU ASP SEQRES 16 B 485 PRO PHE PHE LEU SER ILE THR VAL PHE PRO PHE LEU ILE SEQRES 17 B 485 PRO ILE LEU GLU VAL LEU ASN ILE CYS VAL PHE PRO ARG SEQRES 18 B 485 GLU VAL THR ASN PHE LEU ARG LYS SER VAL LYS ARG MET SEQRES 19 B 485 LYS GLU SER ARG LEU GLU ASP THR GLN LYS HIS ARG VAL SEQRES 20 B 485 ASP PHE LEU GLN LEU MET ILE ASP SER GLN ASN SER LYS SEQRES 21 B 485 GLU THR GLU SER HIS LYS ALA LEU SER ASP LEU GLU LEU SEQRES 22 B 485 VAL ALA GLN SER ILE ILE PHE ILE PHE ALA GLY TYR GLU SEQRES 23 B 485 THR THR SER SER VAL LEU SER PHE ILE MET TYR GLU LEU SEQRES 24 B 485 ALA THR HIS PRO ASP VAL GLN GLN LYS LEU GLN GLU GLU SEQRES 25 B 485 ILE ASP ALA VAL LEU PRO ASN LYS ALA PRO PRO THR TYR SEQRES 26 B 485 ASP THR VAL LEU GLN MET GLU TYR LEU ASP MET VAL VAL SEQRES 27 B 485 ASN GLU THR LEU ARG LEU PHE PRO ILE ALA MET ARG LEU SEQRES 28 B 485 GLU ARG VAL CYS LYS LYS ASP VAL GLU ILE ASN GLY MET SEQRES 29 B 485 PHE ILE PRO LYS GLY VAL VAL VAL MET ILE PRO SER TYR SEQRES 30 B 485 ALA LEU HIS ARG ASP PRO LYS TYR TRP THR GLU PRO GLU SEQRES 31 B 485 LYS PHE LEU PRO GLU ARG PHE SER LYS LYS ASN LYS ASP SEQRES 32 B 485 ASN ILE ASP PRO TYR ILE TYR THR PRO PHE GLY SER GLY SEQRES 33 B 485 PRO ARG ASN CYS ILE GLY MET ARG PHE ALA LEU MET ASN SEQRES 34 B 485 MET LYS LEU ALA LEU ILE ARG VAL LEU GLN ASN PHE SER SEQRES 35 B 485 PHE LYS PRO CYS LYS GLU THR GLN ILE PRO LEU LYS LEU SEQRES 36 B 485 SER LEU GLY GLY LEU LEU GLN PRO GLU LYS PRO VAL VAL SEQRES 37 B 485 LEU LYS VAL GLU SER ARG ASP GLY THR VAL SER GLY ALA SEQRES 38 B 485 HIS HIS HIS HIS HET HEM A1497 43 HET ERY A1498 51 HET HEM B1497 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ERY ERYTHROMYCIN A HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 ERY C37 H67 N O13 FORMUL 6 HOH *49(H2 O) HELIX 1 1 GLY A 31 GLY A 37 1 7 HELIX 2 2 ASN A 49 HIS A 54 5 6 HELIX 3 3 LYS A 55 GLY A 69 1 15 HELIX 4 4 ASP A 86 VAL A 95 1 10 HELIX 5 5 VAL A 111 ALA A 117 5 7 HELIX 6 6 GLU A 122 LEU A 132 1 11 HELIX 7 7 LEU A 133 PHE A 137 5 5 HELIX 8 8 MET A 145 THR A 166 1 22 HELIX 9 9 LEU A 172 GLY A 190 1 19 HELIX 10 10 PHE A 203 ARG A 212 1 10 HELIX 11 11 PHE A 219 PHE A 226 1 8 HELIX 12 12 PHE A 228 LEU A 236 1 9 HELIX 13 13 PRO A 242 SER A 259 1 18 HELIX 14 14 PHE A 271 ASN A 280 1 10 HELIX 15 15 SER A 291 LEU A 339 1 49 HELIX 16 16 THR A 346 LEU A 351 1 6 HELIX 17 17 MET A 353 PHE A 367 1 15 HELIX 18 18 PRO A 397 HIS A 402 1 6 HELIX 19 19 LEU A 415 SER A 420 5 6 HELIX 20 20 ASN A 423 ILE A 427 5 5 HELIX 21 21 SER A 437 ASN A 441 5 5 HELIX 22 22 GLY A 444 ASN A 462 1 19 HELIX 23 23 GLY B 31 GLY B 37 1 7 HELIX 24 24 ASN B 49 HIS B 54 5 6 HELIX 25 25 LYS B 55 GLY B 69 1 15 HELIX 26 26 ASP B 86 VAL B 95 1 10 HELIX 27 27 VAL B 111 ALA B 117 5 7 HELIX 28 28 GLU B 122 LEU B 132 1 11 HELIX 29 29 SER B 134 THR B 138 5 5 HELIX 30 30 LEU B 142 GLU B 144 5 3 HELIX 31 31 MET B 145 THR B 166 1 22 HELIX 32 32 LEU B 172 GLY B 190 1 19 HELIX 33 33 PHE B 203 LYS B 209 1 7 HELIX 34 34 PRO B 218 PHE B 226 1 9 HELIX 35 35 PHE B 228 LEU B 236 1 9 HELIX 36 36 PRO B 242 GLU B 258 1 17 HELIX 37 37 PHE B 271 ILE B 276 1 6 HELIX 38 38 SER B 291 THR B 323 1 33 HELIX 39 39 HIS B 324 LEU B 339 1 16 HELIX 40 40 PRO B 340 ALA B 343 5 4 HELIX 41 41 THR B 346 LEU B 351 1 6 HELIX 42 42 MET B 353 PHE B 367 1 15 HELIX 43 43 PRO B 397 HIS B 402 1 6 HELIX 44 44 LEU B 415 SER B 420 5 6 HELIX 45 45 ASN B 423 ILE B 427 5 5 HELIX 46 46 SER B 437 ASN B 441 5 5 HELIX 47 47 GLY B 444 ASN B 462 1 19 SHEET 1 AA 4 TRP A 72 ASP A 76 0 SHEET 2 AA 4 GLN A 79 ALA A 83 -1 O GLN A 79 N ASP A 76 SHEET 3 AA 4 VAL A 393 ILE A 396 1 O VAL A 393 N LEU A 82 SHEET 4 AA 4 LEU A 373 VAL A 376 -1 O LEU A 373 N ILE A 396 SHEET 1 AB 3 VAL A 170 THR A 171 0 SHEET 2 AB 3 VAL A 490 SER A 495 -1 O LEU A 491 N VAL A 170 SHEET 3 AB 3 PHE A 463 PRO A 467 -1 O SER A 464 N GLU A 494 SHEET 1 AC 2 VAL A 381 GLU A 382 0 SHEET 2 AC 2 PHE A 387 ILE A 388 -1 O ILE A 388 N VAL A 381 SHEET 1 BA 4 VAL B 71 ASP B 76 0 SHEET 2 BA 4 GLN B 79 ILE B 84 -1 O GLN B 79 N ASP B 76 SHEET 3 BA 4 VAL B 393 ILE B 396 1 O VAL B 393 N LEU B 82 SHEET 4 BA 4 LEU B 373 VAL B 376 -1 O LEU B 373 N ILE B 396 SHEET 1 BB 3 VAL B 170 THR B 171 0 SHEET 2 BB 3 VAL B 490 SER B 495 -1 O LEU B 491 N VAL B 170 SHEET 3 BB 3 PHE B 463 LYS B 466 -1 O SER B 464 N GLU B 494 SHEET 1 BC 2 VAL B 381 ILE B 383 0 SHEET 2 BC 2 MET B 386 ILE B 388 -1 O MET B 386 N ILE B 383 LINK SG CYS A 442 FE HEM A1497 1555 1555 2.43 LINK SG CYS B 442 FE HEM B1497 1555 1555 2.06 CISPEP 1 GLY A 109 PRO A 110 0 -8.24 CISPEP 2 ILE A 473 PRO A 474 0 -5.70 CISPEP 3 GLY B 109 PRO B 110 0 -2.84 CISPEP 4 ILE B 473 PRO B 474 0 -4.42 SITE 1 AC1 9 PHE A 57 ARG A 106 PHE A 108 SER A 119 SITE 2 AC1 9 PHE A 220 ALA A 305 ARG A 372 GLU A 374 SITE 3 AC1 9 HEM A1497 SITE 1 AC2 21 ARG A 105 ILE A 118 SER A 119 TRP A 126 SITE 2 AC2 21 ARG A 130 PHE A 137 PHE A 271 ALA A 305 SITE 3 AC2 21 GLY A 306 ARG A 375 PRO A 434 PHE A 435 SITE 4 AC2 21 GLY A 436 SER A 437 ARG A 440 ASN A 441 SITE 5 AC2 21 CYS A 442 ILE A 443 PHE A 447 ALA A 448 SITE 6 AC2 21 ERY A1498 SITE 1 AC3 17 ARG B 105 ILE B 118 SER B 119 TRP B 126 SITE 2 AC3 17 ARG B 130 PHE B 137 ALA B 305 GLY B 306 SITE 3 AC3 17 THR B 309 VAL B 313 ALA B 370 ARG B 375 SITE 4 AC3 17 PRO B 434 PHE B 435 ARG B 440 CYS B 442 SITE 5 AC3 17 ILE B 443 CRYST1 67.254 210.706 161.246 90.00 90.00 90.00 C 2 2 21 16 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 0.014869 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006202 0.00000