HEADER OXIDOREDUCTASE 31-MAR-17 5VCD TITLE CRYSTAL STRUCTURE OF THE CYSTEINE DEPLETED CYP3A4 BOUND TO GLYCEROL 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, GLYCEROL, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.SEVRIOUKOVA REVDAT 6 04-OCT-23 5VCD 1 REMARK REVDAT 5 18-DEC-19 5VCD 1 REMARK REVDAT 4 20-SEP-17 5VCD 1 REMARK REVDAT 3 28-JUN-17 5VCD 1 JRNL REVDAT 2 21-JUN-17 5VCD 1 JRNL REVDAT 1 31-MAY-17 5VCD 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. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1861 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 60.6926 - 4.5845 0.97 2778 159 0.1894 0.2104 REMARK 3 2 4.5845 - 3.6390 1.00 2772 143 0.1662 0.2413 REMARK 3 3 3.6390 - 3.1791 1.00 2752 142 0.1867 0.2461 REMARK 3 4 3.1791 - 2.8884 1.00 2737 147 0.1992 0.2549 REMARK 3 5 2.8884 - 2.6814 1.00 2718 144 0.2062 0.2578 REMARK 3 6 2.6814 - 2.5233 1.00 2730 148 0.2022 0.2699 REMARK 3 7 2.5233 - 2.3969 1.00 2690 139 0.2048 0.2939 REMARK 3 8 2.3969 - 2.2926 1.00 2717 142 0.2101 0.2643 REMARK 3 9 2.2926 - 2.2043 1.00 2718 135 0.2192 0.2709 REMARK 3 10 2.2043 - 2.1282 1.00 2677 134 0.2203 0.2697 REMARK 3 11 2.1282 - 2.0617 1.00 2732 143 0.2424 0.3237 REMARK 3 12 2.0617 - 2.0027 1.00 2707 132 0.2655 0.2942 REMARK 3 13 2.0027 - 1.9500 1.00 2652 153 0.2941 0.3319 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.380 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3918 REMARK 3 ANGLE : 1.149 5301 REMARK 3 CHIRALITY : 0.048 582 REMARK 3 PLANARITY : 0.006 662 REMARK 3 DIHEDRAL : 14.824 1489 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 26:611) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9364 -23.5007 -14.5253 REMARK 3 T TENSOR REMARK 3 T11: 0.3256 T22: 0.3241 REMARK 3 T33: 0.3201 T12: -0.0291 REMARK 3 T13: 0.0832 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.5139 L22: 2.7930 REMARK 3 L33: 1.5356 L12: -1.2078 REMARK 3 L13: -0.4935 L23: 0.7901 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: -0.1469 S13: -0.0839 REMARK 3 S21: 0.1512 S22: -0.0164 S23: -0.0988 REMARK 3 S31: 0.2088 S32: 0.2359 S33: 0.0469 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VCD 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_1000227216. 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 : 37249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 79.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 5VCC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 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 38.23000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.83000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.44500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.23000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.83000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.44500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.23000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.83000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.44500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.23000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.83000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.44500 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: 9320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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 -76.46000 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 72920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -184.0 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 -76.46000 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 -76.46000 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 1 REMARK 465 ALA A 2 REMARK 465 TYR A 23 REMARK 465 LEU A 24 REMARK 465 TYR A 25 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 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 NZ LYS A 66 O HOH A 701 2.04 REMARK 500 OH TYR A 152 ND2 ASN A 192 2.18 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 169 C - N - CA ANGL. DEV. = 11.5 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 20.27 -150.43 REMARK 500 PHE A 46 -55.80 71.53 REMARK 500 VAL A 101 -47.67 -134.14 REMARK 500 PHE A 102 58.62 -106.29 REMARK 500 ASP A 123 -126.72 51.37 REMARK 500 PRO A 169 136.46 -31.90 REMARK 500 PHE A 226 68.00 -119.84 REMARK 500 LEU A 290 108.98 -52.28 REMARK 500 PRO A 340 121.88 -28.95 REMARK 500 ASN A 341 110.11 -29.67 REMARK 500 LYS A 342 7.37 87.24 REMARK 500 MET A 371 -50.77 66.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 340 ASN A 341 -143.28 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 98.3 REMARK 620 3 HEM A 601 NB 90.5 90.1 REMARK 620 4 HEM A 601 NC 89.0 172.7 89.3 REMARK 620 5 HEM A 601 ND 95.5 89.7 174.0 90.2 REMARK 620 6 HOH A 721 O 171.2 86.2 81.9 86.6 92.1 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 GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 613 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: 5VCE RELATED DB: PDB REMARK 900 RELATED ID: 5VCG RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MA ARE THE FIRST TWO RESIDUES, FRAGMENT 3-22 DELETED DBREF 5VCD A 23 503 UNP P08684 CP3A4_HUMAN 23 503 SEQADV 5VCD MET A 1 UNP P08684 SEE REMARK 999 SEQADV 5VCD ALA A 2 UNP P08684 SEE REMARK 999 SEQADV 5VCD ALA A 58 UNP P08684 CYS 58 ENGINEERED MUTATION SEQADV 5VCD MET A 64 UNP P08684 CYS 64 ENGINEERED MUTATION SEQADV 5VCD ALA A 98 UNP P08684 CYS 98 ENGINEERED MUTATION SEQADV 5VCD THR A 239 UNP P08684 CYS 239 ENGINEERED MUTATION SEQADV 5VCD ALA A 377 UNP P08684 CYS 377 ENGINEERED MUTATION SEQADV 5VCD SER A 468 UNP P08684 CYS 468 ENGINEERED MUTATION SEQADV 5VCD HIS A 504 UNP P08684 EXPRESSION TAG SEQADV 5VCD HIS A 505 UNP P08684 EXPRESSION TAG SEQADV 5VCD HIS A 506 UNP P08684 EXPRESSION TAG SEQADV 5VCD 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 GOL A 602 6 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET GOL A 608 6 HET GOL A 609 6 HET GOL A 610 6 HET GOL A 611 6 HET GOL A 612 6 HET GOL A 613 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 GOL 12(C3 H8 O3) FORMUL 15 HOH *106(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 HIS A 54 5 6 HELIX 4 AA4 LYS A 55 GLY A 69 1 15 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 THR A 166 1 29 HELIX 10 AB1 LEU A 172 PHE A 189 1 18 HELIX 11 AB2 ASP A 201 LYS A 208 1 8 HELIX 12 AB3 ASP A 217 PHE A 226 1 10 HELIX 13 AB4 LEU A 229 LEU A 236 1 8 HELIX 14 AB5 PRO A 242 LEU A 261 1 20 HELIX 15 AB6 ASP A 270 ASN A 280 1 11 HELIX 16 AB7 SER A 291 HIS A 324 1 34 HELIX 17 AB8 HIS A 324 LEU A 339 1 16 HELIX 18 AB9 PRO A 340 ALA A 343 5 4 HELIX 19 AC1 THR A 346 LEU A 351 1 6 HELIX 20 AC2 MET A 353 PHE A 367 1 15 HELIX 21 AC3 PRO A 397 ARG A 403 1 7 HELIX 22 AC4 LEU A 415 SER A 420 5 6 HELIX 23 AC5 ASN A 423 ILE A 427 5 5 HELIX 24 AC6 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 ARG A 375 O VAL A 394 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 2.41 LINK FE HEM A 601 O HOH A 721 1555 1555 2.45 CISPEP 1 GLY A 109 PRO A 110 0 -1.62 CISPEP 2 LEU A 261 GLU A 262 0 -6.21 CISPEP 3 ILE A 473 PRO A 474 0 -3.75 SITE 1 AC1 24 ARG A 105 ILE A 118 SER A 119 TRP A 126 SITE 2 AC1 24 ARG A 130 PHE A 137 PHE A 302 ALA A 305 SITE 3 AC1 24 GLY A 306 THR A 309 ILE A 369 ALA A 370 SITE 4 AC1 24 LEU A 373 ARG A 375 PRO A 434 PHE A 435 SITE 5 AC1 24 GLY A 436 SER A 437 ARG A 440 ASN A 441 SITE 6 AC1 24 CYS A 442 ILE A 443 HOH A 721 HOH A 764 SITE 1 AC2 7 SER A 119 ARG A 212 PHE A 304 ALA A 305 SITE 2 AC2 7 HOH A 721 HOH A 727 HOH A 765 SITE 1 AC3 7 PHE A 33 GLY A 40 THR A 42 GLN A 329 SITE 2 AC3 7 HOH A 708 HOH A 716 HOH A 725 SITE 1 AC4 8 PRO A 41 THR A 42 LEU A 44 ASN A 49 SITE 2 AC4 8 LEU A 51 SER A 52 HOH A 733 HOH A 750 SITE 1 AC5 10 LYS A 55 GLY A 56 PHE A 57 ALA A 58 SITE 2 AC5 10 MET A 59 MET A 371 SER A 478 GLY A 480 SITE 3 AC5 10 LEU A 482 LEU A 483 SITE 1 AC6 8 TYR A 53 PHE A 57 ASP A 76 ARG A 106 SITE 2 AC6 8 PHE A 215 PHE A 220 THR A 224 ARG A 372 SITE 1 AC7 3 TYR A 407 THR A 409 ARG A 418 SITE 1 AC8 6 LYS A 34 LYS A 35 HIS A 324 PRO A 325 SITE 2 AC8 6 ASP A 326 HOH A 735 SITE 1 AC9 4 LYS A 330 GLU A 354 MET A 358 GLU A 417 SITE 1 AD1 5 LYS A 209 LEU A 210 LEU A 211 PHE A 213 SITE 2 AD1 5 PRO A 242 SITE 1 AD2 4 LYS A 67 GLN A 332 GLU A 333 ARG A 496 SITE 1 AD3 4 PRO A 405 LYS A 406 TYR A 407 THR A 409 SITE 1 AD4 5 GLU A 308 SER A 311 SER A 312 GLN A 484 SITE 2 AD4 5 PRO A 485 CRYST1 76.460 99.660 132.890 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 0.013079 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007525 0.00000