Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH (+)-3-CARENE
 
Authors :  M. B. Shah
Date :  06 Nov 14  (Deposition) - 28 Jan 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  P450, Cytochrome P450 2B6, Monooxygenase, Membrane Protein, Cyp2B6, Endoplasmic Reticulum, Heme, Iron, Metal Binding, Microsome, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shah, P. R. Wilderman, J. Liu, H. H. Jang, Q. Zhang, C. D. Stout, J. R. Halpert
Structural And Biophysical Characterization Of Human Cytochromes P450 2B6 And 2A6 Bound To Volatile Hydrocarbons Analysis And Comparison.
Mol. Pharmacol. V. 87 649 2015
PubMed-ID: 25585967  |  Reference-DOI: 10.1124/MOL.114.097014

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B6
    Chains: A, B
    EC Number: 1.14.13.-, 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYP2B6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1,4-CINEOLE 2-EXO-MONOOXYGENASE, CYPIIB6, CYTOCHROME P450 IIB1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
13V42Ligand/Ion(+)-3-CARENE
2CM56Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3GOL2Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
13V41Ligand/Ion(+)-3-CARENE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3GOL2Ligand/IonGLYCEROL
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
13V41Ligand/Ion(+)-3-CARENE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3GOL-1Ligand/IonGLYCEROL
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , ILE A:179 , ALA A:298 , THR A:302 , THR A:306 , LEU A:362 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , 3V4 A:502 , HOH A:663BINDING SITE FOR RESIDUE HEM A 501
02AC2SOFTWAREPHE A:297 , ALA A:298 , THR A:302 , VAL A:367 , HEM A:501BINDING SITE FOR RESIDUE 3V4 A 502
03AC3SOFTWAREPHE A:220 , PHE A:223BINDING SITE FOR RESIDUE CM5 A 503
04AC4SOFTWAREGLU A:194 , MET A:198 , PHE A:202 , TYR A:244 , PHE A:296BINDING SITE FOR RESIDUE CM5 A 504
05AC5SOFTWARELEU A:43 , MET A:46 , ARG A:48 , GLY A:50 , GLN A:215BINDING SITE FOR RESIDUE CM5 A 505
06AC6SOFTWAREHOH A:790BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWAREHOH A:789BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWAREARG B:98 , VAL B:113 , ILE B:114 , TRP B:121 , ARG B:125 , ILE B:179 , ALA B:298 , THR B:302 , THR B:306 , GLN B:357 , LEU B:362 , HIS B:369 , LEU B:392 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , 3V4 B:502 , HOH B:612BINDING SITE FOR RESIDUE HEM B 501
09AC9SOFTWAREPHE B:297 , ALA B:298 , VAL B:367 , HEM B:501BINDING SITE FOR RESIDUE 3V4 B 502
10BC1SOFTWAREPHE B:220 , PHE B:223BINDING SITE FOR RESIDUE CM5 B 503
11BC2SOFTWARELYS A:384 , HOH A:810 , GLU B:194 , MET B:198 , PHE B:202 , TYR B:244 , HIS B:247 , PHE B:296 , HOH B:796BINDING SITE FOR RESIDUE CM5 B 504
12BC3SOFTWARELEU B:43 , MET B:46 , ASP B:47 , ARG B:48BINDING SITE FOR RESIDUE CM5 B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RRT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RRT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RRT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RRT)

(-) Exons   (0, 0)

(no "Exon" information available for 4RRT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrt A  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR 491
                                    37        47        57        67        77        87        97       107       117       127       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
                                                                                                                                     135|                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                      139                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrt B  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR 491
                                    37        47        57        67        77        87        97       107       117       127       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
                                                                                                                                     135|                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                      139
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4RRT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RRT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RRT)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3V4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CM5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rrt)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4rrt
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CP2B6_HUMAN | P20813
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.13.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.14.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CP2B6_HUMAN | P20813
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CP2B6_HUMAN | P20813: 3ibd 3qoa 3qu8 3ua5 4i91 4rql 4zv8 5uap 5uda 5uec 5ufg

(-) Related Entries Specified in the PDB File

3ibd CRYSTAL STRUCTURE OF A CYTOCHROME P450 2B6 GENETIC VARIANT IN COMPLEX WITH THE INHIBITOR 4-(4-CHLOROPHENYL)IMIDAZOLE
3qoa CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH THE INHIBITOR 4-BENZYLPYRIDINE
3qu8 CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH THE INHIBITOR 4-(4-NITROBENZYL)PYRIDINE
3ua5 CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH TWO MOLECULES OF AMLODIPINE
4i91 CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH ALPHA-PINENE
4rql CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH SABINENE