HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 27-NOV-12 4I4G TITLE CRYSTAL STRUCTURE OF CYP3A4 LIGATED TO OXAZOLE-SUBSTITUTED TITLE 2 DESOXYRITONAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 3A4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,8-CINEOLE 2-EXO-MONOOXYGENASE, ALBENDAZOLE MONOOXYGENASE, COMPND 5 ALBENDAZOLE SULFOXIDASE, CYPIIIA3, CYPIIIA4, CYTOCHROME P450 3A3, COMPND 6 CYTOCHROME P450 HLP, CYTOCHROME P450 NF-25, CYTOCHROME P450-PCN1, COMPND 7 NIFEDIPINE OXIDASE, QUININE 3-MONOOXYGENASE, TAUROCHENODEOXYCHOLATE COMPND 8 6-ALPHA-HYDROXYLASE; COMPND 9 EC: 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CYP3A4, CYP3A3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PCWORI KEYWDS MONOOXYGENASE, CYTOCHROME P450 REDUCTASE, CYTOCHROME B5, ENDOPLASMIC KEYWDS 2 RETICULUM, CYTOCHROME P450, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.F.SEVRIOUKOVA,T.L.POULOS REVDAT 4 20-SEP-23 4I4G 1 REMARK SEQADV LINK REVDAT 3 22-MAY-13 4I4G 1 JRNL REVDAT 2 01-MAY-13 4I4G 1 JRNL REVDAT 1 24-APR-13 4I4G 0 JRNL AUTH I.F.SEVRIOUKOVA,T.L.POULOS JRNL TITL PYRIDINE-SUBSTITUTED DESOXYRITONAVIR IS A MORE POTENT JRNL TITL 2 INHIBITOR OF CYTOCHROME P450 3A4 THAN RITONAVIR. JRNL REF J.MED.CHEM. V. 56 3733 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23586711 JRNL DOI 10.1021/JM400288Z REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12710 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 661 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) : 2.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 863 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3695 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.408 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.312 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.958 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3886 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5270 ; 1.894 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 456 ; 6.281 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;35.740 ;23.851 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 690 ;20.592 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;23.294 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 580 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2901 ; 0.007 ; 0.021 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 705 REMARK 3 ORIGIN FOR THE GROUP (A): -19.0826 23.6054 -12.6565 REMARK 3 T TENSOR REMARK 3 T11: 0.1028 T22: 0.1798 REMARK 3 T33: 0.1081 T12: -0.0178 REMARK 3 T13: -0.0311 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 1.5506 L22: 4.0551 REMARK 3 L33: 1.9179 L12: -1.0947 REMARK 3 L13: 0.2718 L23: -0.6635 REMARK 3 S TENSOR REMARK 3 S11: -0.1527 S12: 0.0648 S13: 0.2591 REMARK 3 S21: 0.5460 S22: 0.0659 S23: -0.2421 REMARK 3 S31: -0.3008 S32: 0.0871 S33: 0.0867 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4I4G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12236 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.718 REMARK 200 RESOLUTION RANGE LOW (A) : 49.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3NXU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM MALONATE, PH 6.0, REMARK 280 MICROBATCH UNDER OIL, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 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 0.00000 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 38.32750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.79250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.18750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.32750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.79250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.18750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.32750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.79250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.18750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.32750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.79250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.18750 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 74970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 21 REMARK 465 ALA A 22 REMARK 465 TYR A 23 REMARK 465 LEU A 24 REMARK 465 TYR A 25 REMARK 465 GLY A 26 REMARK 465 GLN A 265 REMARK 465 LYS A 266 REMARK 465 HIS A 267 REMARK 465 SER A 281 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 HIS A 287 REMARK 465 LYS A 288 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 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 ARG A 375 NE - CZ - NH1 ANGL. DEV. = 3.4 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 HIS A 28 -73.77 103.53 REMARK 500 SER A 29 -7.76 -56.67 REMARK 500 PHE A 46 -54.73 68.24 REMARK 500 PHE A 102 74.08 -105.08 REMARK 500 LYS A 115 -39.68 -38.84 REMARK 500 ASP A 123 -132.49 49.98 REMARK 500 PHE A 137 57.98 -111.99 REMARK 500 ASP A 194 10.51 55.55 REMARK 500 THR A 207 -72.68 -61.54 REMARK 500 LYS A 208 -14.03 -48.28 REMARK 500 LYS A 209 40.04 -94.33 REMARK 500 ARG A 243 -14.96 -41.38 REMARK 500 THR A 246 0.26 -62.01 REMARK 500 ASP A 270 -161.76 -125.98 REMARK 500 SER A 291 -158.69 -104.03 REMARK 500 GLU A 410 63.24 39.13 REMARK 500 ASN A 426 15.55 -67.54 REMARK 500 ASN A 441 -179.41 -62.41 REMARK 500 CYS A 468 -168.55 -104.36 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 A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 442 SG REMARK 620 2 HEM A 601 NA 105.1 REMARK 620 3 HEM A 601 NB 93.0 84.7 REMARK 620 4 HEM A 601 NC 108.2 146.5 90.4 REMARK 620 5 HEM A 601 ND 103.4 86.6 163.0 88.9 REMARK 620 6 Z8Z A 602 N35 175.4 72.6 82.9 74.0 80.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE Z8Z A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NXU RELATED DB: PDB REMARK 900 CYP3A4-RITONAVIR COMPLEX DBREF 4I4G A 21 503 UNP P08684 CP3A4_HUMAN 1 503 SEQADV 4I4G A UNP P08684 LEU 3 DELETION SEQADV 4I4G A UNP P08684 ILE 4 DELETION SEQADV 4I4G A UNP P08684 PRO 5 DELETION SEQADV 4I4G A UNP P08684 ASP 6 DELETION SEQADV 4I4G A UNP P08684 LEU 7 DELETION SEQADV 4I4G A UNP P08684 ALA 8 DELETION SEQADV 4I4G A UNP P08684 MET 9 DELETION SEQADV 4I4G A UNP P08684 GLU 10 DELETION SEQADV 4I4G A UNP P08684 THR 11 DELETION SEQADV 4I4G A UNP P08684 TRP 12 DELETION SEQADV 4I4G A UNP P08684 LEU 13 DELETION SEQADV 4I4G A UNP P08684 LEU 14 DELETION SEQADV 4I4G A UNP P08684 LEU 15 DELETION SEQADV 4I4G A UNP P08684 ALA 16 DELETION SEQADV 4I4G A UNP P08684 VAL 17 DELETION SEQADV 4I4G A UNP P08684 SER 18 DELETION SEQADV 4I4G A UNP P08684 LEU 19 DELETION SEQADV 4I4G A UNP P08684 VAL 20 DELETION SEQADV 4I4G A UNP P08684 LEU 21 DELETION SEQADV 4I4G A UNP P08684 LEU 22 DELETION SEQADV 4I4G HIS A 504 UNP P08684 EXPRESSION TAG SEQADV 4I4G HIS A 505 UNP P08684 EXPRESSION TAG SEQADV 4I4G HIS A 506 UNP P08684 EXPRESSION TAG SEQADV 4I4G HIS A 507 UNP P08684 EXPRESSION TAG SEQRES 1 A 487 MET ALA TYR LEU TYR GLY THR HIS SER HIS GLY LEU PHE SEQRES 2 A 487 LYS LYS LEU GLY ILE PRO GLY PRO THR PRO LEU PRO PHE SEQRES 3 A 487 LEU GLY ASN ILE LEU SER TYR HIS LYS GLY PHE CYS MET SEQRES 4 A 487 PHE ASP MET GLU CYS HIS LYS LYS TYR GLY LYS VAL TRP SEQRES 5 A 487 GLY PHE TYR ASP GLY GLN GLN PRO VAL LEU ALA ILE THR SEQRES 6 A 487 ASP PRO ASP MET ILE LYS THR VAL LEU VAL LYS GLU CYS SEQRES 7 A 487 TYR SER VAL PHE THR ASN ARG ARG PRO PHE GLY PRO VAL SEQRES 8 A 487 GLY PHE MET LYS SER ALA ILE SER ILE ALA GLU ASP GLU SEQRES 9 A 487 GLU TRP LYS ARG LEU ARG SER LEU LEU SER PRO THR PHE SEQRES 10 A 487 THR SER GLY LYS LEU LYS GLU MET VAL PRO ILE ILE ALA SEQRES 11 A 487 GLN TYR GLY ASP VAL LEU VAL ARG ASN LEU ARG ARG GLU SEQRES 12 A 487 ALA GLU THR GLY LYS PRO VAL THR LEU LYS ASP VAL PHE SEQRES 13 A 487 GLY ALA TYR SER MET ASP VAL ILE THR SER THR SER PHE SEQRES 14 A 487 GLY VAL ASN ILE ASP SER LEU ASN ASN PRO GLN ASP PRO SEQRES 15 A 487 PHE VAL GLU ASN THR LYS LYS LEU LEU ARG PHE ASP PHE SEQRES 16 A 487 LEU ASP PRO PHE PHE LEU SER ILE THR VAL PHE PRO PHE SEQRES 17 A 487 LEU ILE PRO ILE LEU GLU VAL LEU ASN ILE CYS VAL PHE SEQRES 18 A 487 PRO ARG GLU VAL THR ASN PHE LEU ARG LYS SER VAL LYS SEQRES 19 A 487 ARG MET LYS GLU SER ARG LEU GLU ASP THR GLN LYS HIS SEQRES 20 A 487 ARG VAL ASP PHE LEU GLN LEU MET ILE ASP SER GLN ASN SEQRES 21 A 487 SER LYS GLU THR GLU SER HIS LYS ALA LEU SER ASP LEU SEQRES 22 A 487 GLU LEU VAL ALA GLN SER ILE ILE PHE ILE PHE ALA GLY SEQRES 23 A 487 TYR GLU THR THR SER SER VAL LEU SER PHE ILE MET TYR SEQRES 24 A 487 GLU LEU ALA THR HIS PRO ASP VAL GLN GLN LYS LEU GLN SEQRES 25 A 487 GLU GLU ILE ASP ALA VAL LEU PRO ASN LYS ALA PRO PRO SEQRES 26 A 487 THR TYR ASP THR VAL LEU GLN MET GLU TYR LEU ASP MET SEQRES 27 A 487 VAL VAL ASN GLU THR LEU ARG LEU PHE PRO ILE ALA MET SEQRES 28 A 487 ARG LEU GLU ARG VAL CYS LYS LYS ASP VAL GLU ILE ASN SEQRES 29 A 487 GLY MET PHE ILE PRO LYS GLY VAL VAL VAL MET ILE PRO SEQRES 30 A 487 SER TYR ALA LEU HIS ARG ASP PRO LYS TYR TRP THR GLU SEQRES 31 A 487 PRO GLU LYS PHE LEU PRO GLU ARG PHE SER LYS LYS ASN SEQRES 32 A 487 LYS ASP ASN ILE ASP PRO TYR ILE TYR THR PRO PHE GLY SEQRES 33 A 487 SER GLY PRO ARG ASN CYS ILE GLY MET ARG PHE ALA LEU SEQRES 34 A 487 MET ASN MET LYS LEU ALA LEU ILE ARG VAL LEU GLN ASN SEQRES 35 A 487 PHE SER PHE LYS PRO CYS LYS GLU THR GLN ILE PRO LEU SEQRES 36 A 487 LYS LEU SER LEU GLY GLY LEU LEU GLN PRO GLU LYS PRO SEQRES 37 A 487 VAL VAL LEU LYS VAL GLU SER ARG ASP GLY THR VAL SER SEQRES 38 A 487 GLY ALA HIS HIS HIS HIS HET HEM A 601 43 HET Z8Z A 602 49 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM Z8Z N~2~-(METHYL{[2-(PROPAN-2-YL)-1,3-THIAZOL-4- HETNAM 2 Z8Z YL]METHYL}CARBAMOYL)-N-[(2R,5R)-5-{[(1,3-OXAZOL-5- HETNAM 3 Z8Z YLMETHOXY)CARBONYL]AMINO}-1,6-DIPHENYLHEXAN-2-YL]-L- HETNAM 4 Z8Z VALINAMIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 Z8Z C37 H48 N6 O5 S FORMUL 4 HOH *5(H2 O) HELIX 1 1 HIS A 28 HIS A 30 5 3 HELIX 2 2 GLY A 31 GLY A 37 1 7 HELIX 3 3 ASN A 49 LYS A 55 5 7 HELIX 4 4 GLY A 56 GLY A 69 1 14 HELIX 5 5 ASP A 86 VAL A 95 1 10 HELIX 6 6 VAL A 111 ALA A 117 5 7 HELIX 7 7 GLU A 122 SER A 134 1 13 HELIX 8 8 PRO A 135 PHE A 137 5 3 HELIX 9 9 THR A 138 GLU A 144 1 7 HELIX 10 10 MET A 145 GLY A 167 1 23 HELIX 11 11 LEU A 172 GLY A 190 1 19 HELIX 12 12 ASP A 194 ASN A 198 5 5 HELIX 13 13 ASP A 201 LYS A 209 1 9 HELIX 14 14 PHE A 219 PHE A 226 1 8 HELIX 15 15 LEU A 229 LEU A 236 1 8 HELIX 16 16 GLU A 244 ASP A 263 1 20 HELIX 17 17 ASP A 270 GLN A 279 1 10 HELIX 18 18 ASP A 292 HIS A 324 1 33 HELIX 19 19 HIS A 324 LEU A 339 1 16 HELIX 20 20 THR A 346 MET A 353 1 8 HELIX 21 21 MET A 353 PHE A 367 1 15 HELIX 22 22 PRO A 397 HIS A 402 1 6 HELIX 23 23 LEU A 415 SER A 420 5 6 HELIX 24 24 SER A 437 ASN A 441 5 5 HELIX 25 25 GLY A 444 GLN A 461 1 18 SHEET 1 A 4 VAL A 71 ASP A 76 0 SHEET 2 A 4 GLN A 79 ILE A 84 -1 O VAL A 81 N PHE A 74 SHEET 3 A 4 VAL A 393 ILE A 396 1 O VAL A 393 N LEU A 82 SHEET 4 A 4 LEU A 373 VAL A 376 -1 N LEU A 373 O ILE A 396 SHEET 1 B 3 VAL A 170 THR A 171 0 SHEET 2 B 3 VAL A 490 SER A 495 -1 O LEU A 491 N VAL A 170 SHEET 3 B 3 PHE A 463 LYS A 466 -1 N LYS A 466 O LYS A 492 SHEET 1 C 2 VAL A 381 GLU A 382 0 SHEET 2 C 2 PHE A 387 ILE A 388 -1 O ILE A 388 N VAL A 381 LINK SG CYS A 442 FE HEM A 601 1555 1555 2.13 LINK FE HEM A 601 N35 Z8Z A 602 1555 1555 2.10 CISPEP 1 ILE A 473 PRO A 474 0 -5.44 SITE 1 AC1 22 ARG A 105 ILE A 118 SER A 119 TRP A 126 SITE 2 AC1 22 ARG A 130 ALA A 305 THR A 309 ILE A 369 SITE 3 AC1 22 ALA A 370 ARG A 375 PRO A 434 PHE A 435 SITE 4 AC1 22 GLY A 436 SER A 437 ARG A 440 ASN A 441 SITE 5 AC1 22 CYS A 442 ILE A 443 GLY A 444 PHE A 447 SITE 6 AC1 22 MET A 452 Z8Z A 602 SITE 1 AC2 16 ASP A 76 ARG A 106 PHE A 108 SER A 119 SITE 2 AC2 16 ILE A 120 LEU A 210 LEU A 211 PHE A 213 SITE 3 AC2 16 THR A 224 PHE A 241 ILE A 301 PHE A 304 SITE 4 AC2 16 ALA A 305 THR A 309 GLU A 374 HEM A 601 CRYST1 76.655 99.585 126.375 90.00 90.00 90.00 I 2 2 2 8 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 0.013045 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007913 0.00000