HEADER OXIDOREDUCTASE/INHIBITOR 31-MAR-17 5VCE TITLE CRYSTAL STRUCTURE OF THE CYSTEINE DEPLETED CYP3A4 BOUND TO RITONAVIR 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,CHOLESTEROL 25-HYDROXYLASE, COMPND 6 CYTOCHROME P450 3A3,CYTOCHROME P450 HLP,CYTOCHROME P450 NF-25, COMPND 7 CYTOCHROME P450-PCN1,NIFEDIPINE OXIDASE,QUININE 3-MONOOXYGENASE, COMPND 8 TAUROCHENODEOXYCHOLATE 6-ALPHA-HYDROXYLASE; COMPND 9 EC: 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.9; 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: 562 KEYWDS CYTOCHROME P450, CYP3A4, MONOOXYGENASE, CYSTEINE MUTATION, RITONAVIR, KEYWDS 2 OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.SEVRIOUKOVA REVDAT 7 04-OCT-23 5VCE 1 REMARK REVDAT 6 18-DEC-19 5VCE 1 REMARK REVDAT 5 20-SEP-17 5VCE 1 REMARK REVDAT 4 28-JUN-17 5VCE 1 JRNL REVDAT 3 21-JUN-17 5VCE 1 JRNL REVDAT 2 14-JUN-17 5VCE 1 REMARK REVDAT 1 31-MAY-17 5VCE 0 JRNL AUTH I.F.SEVRIOUKOVA JRNL TITL HIGH-LEVEL PRODUCTION AND PROPERTIES OF THE JRNL TITL 2 CYSTEINE-DEPLETED CYTOCHROME P450 3A4. JRNL REF BIOCHEMISTRY V. 56 3058 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28590129 JRNL DOI 10.1021/ACS.BIOCHEM.7B00334 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 24498 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) : 0.240 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1318 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1803 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3676 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.85000 REMARK 3 B22 (A**2) : 1.56000 REMARK 3 B33 (A**2) : -3.42000 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): 0.347 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.244 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.255 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.986 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3902 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5295 ; 1.381 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 461 ; 5.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;34.666 ;23.851 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 694 ;17.981 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.326 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2905 ; 0.006 ; 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): 1841 ; 2.910 ; 5.073 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2297 ; 4.592 ; 7.593 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2056 ; 3.217 ; 5.393 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): 6196 ;10.188 ;43.734 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 26 A 602 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2220 26.6779 142.5575 REMARK 3 T TENSOR REMARK 3 T11: 0.0511 T22: 0.0855 REMARK 3 T33: 0.3021 T12: 0.0312 REMARK 3 T13: 0.0253 T23: 0.0636 REMARK 3 L TENSOR REMARK 3 L11: 1.0652 L22: 2.6250 REMARK 3 L33: 0.5801 L12: 1.2517 REMARK 3 L13: -0.6986 L23: -0.7747 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: -0.1008 S13: -0.0818 REMARK 3 S21: -0.2246 S22: -0.1222 S23: 0.1030 REMARK 3 S31: 0.0055 S32: 0.0058 S33: 0.1438 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: NULL REMARK 4 REMARK 4 5VCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 79.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 5VCC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, PH 7.5, MICROBATCH, REMARK 280 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 38.68500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.35500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.61000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.35500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.61000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.35500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.61000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.68500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.35500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.61000 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: 6460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 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 77.37000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 100.71000 REMARK 350 BIOMT3 2 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: 16630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 72600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -214.0 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 77.37000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 100.71000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 77.37000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 258.44000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 100.71000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 258.44000 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 1 REMARK 465 ALA A 2 REMARK 465 TYR A 23 REMARK 465 LEU A 24 REMARK 465 TYR A 25 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 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 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: 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 O PHE A 248 OG SER A 252 1.85 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 PRO A 340 C - N - CA ANGL. DEV. = 10.9 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 THR A 27 21.79 -156.01 REMARK 500 PHE A 46 -50.79 73.03 REMARK 500 VAL A 95 -74.53 -121.11 REMARK 500 VAL A 101 -59.20 -138.39 REMARK 500 PHE A 102 57.26 -100.76 REMARK 500 ASP A 123 -116.41 45.65 REMARK 500 PRO A 169 138.46 -32.79 REMARK 500 ASP A 194 93.07 -69.26 REMARK 500 ASN A 198 61.23 -109.90 REMARK 500 PHE A 228 0.76 -60.88 REMARK 500 LYS A 257 70.99 -113.95 REMARK 500 GLU A 258 -160.91 -165.43 REMARK 500 SER A 259 3.42 -59.91 REMARK 500 VAL A 269 33.93 -99.09 REMARK 500 PRO A 340 -111.99 -15.54 REMARK 500 MET A 371 -51.92 73.58 REMARK 500 ASN A 384 37.42 38.22 REMARK 500 SER A 478 121.99 -37.88 REMARK 500 LEU A 479 3.73 -67.74 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 94.9 REMARK 620 3 HEM A 601 NB 85.8 87.5 REMARK 620 4 HEM A 601 NC 84.3 178.9 91.5 REMARK 620 5 HEM A 601 ND 92.7 91.1 177.9 89.8 REMARK 620 6 RIT A 602 N5 168.7 96.4 95.7 84.4 86.1 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: RITONAVIR REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 RIT A 602 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: 013 015 VAL 019 REMARK 630 DETAILS: NULL 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 RIT A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VC0 RELATED DB: PDB REMARK 900 RELATED ID: 5VCC RELATED DB: PDB REMARK 900 RELATED ID: 5VCD RELATED DB: PDB REMARK 900 RELATED ID: 5VCG RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MET ALA ARE THE FIRST TWO RESIDUES, THE FRAGMENT 3-22 WAS DELETED DBREF 5VCE A 23 503 UNP P08684 CP3A4_HUMAN 23 503 SEQADV 5VCE MET A 1 UNP P08684 SEE REMARK 999 SEQADV 5VCE ALA A 2 UNP P08684 SEE REMARK 999 SEQADV 5VCE ALA A 58 UNP P08684 CYS 58 ENGINEERED MUTATION SEQADV 5VCE MET A 64 UNP P08684 CYS 64 ENGINEERED MUTATION SEQADV 5VCE ALA A 98 UNP P08684 CYS 98 ENGINEERED MUTATION SEQADV 5VCE THR A 239 UNP P08684 CYS 239 ENGINEERED MUTATION SEQADV 5VCE ALA A 377 UNP P08684 CYS 377 ENGINEERED MUTATION SEQADV 5VCE SER A 468 UNP P08684 CYS 468 ENGINEERED MUTATION SEQADV 5VCE HIS A 504 UNP P08684 EXPRESSION TAG SEQADV 5VCE HIS A 505 UNP P08684 EXPRESSION TAG SEQADV 5VCE HIS A 506 UNP P08684 EXPRESSION TAG SEQADV 5VCE 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 ALA MET SEQRES 4 A 487 PHE ASP MET GLU MET 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 ALA 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 THR 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 ALA 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 SER 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 RIT A 602 50 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM RIT RITONAVIR HETSYN HEM HEME HETSYN RIT A-84538 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 RIT C37 H48 N6 O5 S2 FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 THR A 27 HIS A 30 5 4 HELIX 2 AA2 GLY A 31 LEU A 36 1 6 HELIX 3 AA3 ASN A 49 LYS A 55 5 7 HELIX 4 AA4 GLY A 56 GLY A 69 1 14 HELIX 5 AA5 ASP A 86 VAL A 95 1 10 HELIX 6 AA6 GLY A 112 ALA A 117 5 6 HELIX 7 AA7 GLU A 122 SER A 134 1 13 HELIX 8 AA8 PRO A 135 PHE A 137 5 3 HELIX 9 AA9 THR A 138 MET A 145 1 8 HELIX 10 AB1 MET A 145 ALA A 150 1 6 HELIX 11 AB2 ALA A 150 GLU A 163 1 14 HELIX 12 AB3 LEU A 172 GLY A 190 1 19 HELIX 13 AB4 ASP A 201 LYS A 209 1 9 HELIX 14 AB5 ASP A 217 PHE A 226 1 10 HELIX 15 AB6 LEU A 229 LEU A 236 1 8 HELIX 16 AB7 PRO A 242 VAL A 253 1 12 HELIX 17 AB8 ASP A 270 ASP A 277 1 8 HELIX 18 AB9 SER A 291 HIS A 324 1 34 HELIX 19 AC1 HIS A 324 LEU A 339 1 16 HELIX 20 AC2 THR A 346 MET A 353 1 8 HELIX 21 AC3 MET A 353 PHE A 367 1 15 HELIX 22 AC4 PRO A 397 HIS A 402 1 6 HELIX 23 AC5 LEU A 415 PHE A 419 5 5 HELIX 24 AC6 SER A 420 ASP A 425 1 6 HELIX 25 AC7 SER A 437 ASN A 441 5 5 HELIX 26 AC8 GLY A 444 ASN A 462 1 19 SHEET 1 AA1 4 VAL A 71 ASP A 76 0 SHEET 2 AA1 4 GLN A 79 ILE A 84 -1 O VAL A 81 N PHE A 74 SHEET 3 AA1 4 VAL A 393 ILE A 396 1 O VAL A 393 N LEU A 82 SHEET 4 AA1 4 LEU A 373 VAL A 376 -1 N LEU A 373 O ILE A 396 SHEET 1 AA2 3 VAL A 170 THR A 171 0 SHEET 2 AA2 3 VAL A 490 SER A 495 -1 O LEU A 491 N VAL A 170 SHEET 3 AA2 3 PHE A 463 PRO A 467 -1 N SER A 464 O GLU A 494 SHEET 1 AA3 2 VAL A 381 ILE A 383 0 SHEET 2 AA3 2 MET A 386 ILE A 388 -1 O ILE A 388 N VAL A 381 LINK SG CYS A 442 FE HEM A 601 1555 1555 2.33 LINK FE HEM A 601 N5 RIT A 602 1555 1555 1.97 CISPEP 1 GLY A 109 PRO A 110 0 1.97 CISPEP 2 LYS A 257 GLU A 258 0 0.00 CISPEP 3 ILE A 473 PRO A 474 0 -2.32 SITE 1 AC1 25 ARG A 105 ILE A 118 TRP A 126 ARG A 130 SITE 2 AC1 25 PHE A 137 PHE A 302 ALA A 305 GLY A 306 SITE 3 AC1 25 THR A 309 VAL A 313 ILE A 369 ALA A 370 SITE 4 AC1 25 ARG A 375 PRO A 434 PHE A 435 GLY A 436 SITE 5 AC1 25 SER A 437 ARG A 440 ASN A 441 CYS A 442 SITE 6 AC1 25 ILE A 443 GLY A 444 MET A 452 RIT A 602 SITE 7 AC1 25 HOH A 714 SITE 1 AC2 16 PRO A 107 PHE A 108 SER A 119 ILE A 120 SITE 2 AC2 16 ARG A 212 PHE A 213 PHE A 215 ILE A 223 SITE 3 AC2 16 THR A 224 PHE A 241 ILE A 301 PHE A 304 SITE 4 AC2 16 ALA A 305 ILE A 369 ALA A 370 HEM A 601 CRYST1 77.370 100.710 129.220 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 0.012925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007739 0.00000