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 CYP2B6 (Y226H/K262R) IN COMPLEX WITH BORNYL BROMIDE
 
Authors :  M. B. Shah, J. R. Halpert
Date :  19 Dec 16  (Deposition) - 12 Apr 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P450, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shah, J. Liu, Q. Zhang, C. D. Stout, J. R. Halpert
Halogen-Pi Interactions In The Cytochrome P450 Active Site: Structural Insights Into Human Cyp2B6 Substrate Selectivity
Acs Chem. Biol. V. 12 1204 2017
PubMed-ID: 28368100  |  Reference-DOI: 10.1021/ACSCHEMBIO.7B00056

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B6
    Chains: A, B
    EC Number: 1.14.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKDH
    Expression System Strain: JM109
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 30-491
    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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
182S2Ligand/Ion(1R,2R,4R)-2-BROMO-1,7,7-TRIMETHYLBICYCLO[2.2.1]HEPTANE
2CM56Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
182S1Ligand/Ion(1R,2R,4R)-2-BROMO-1,7,7-TRIMETHYLBICYCLO[2.2.1]HEPTANE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
182S1Ligand/Ion(1R,2R,4R)-2-BROMO-1,7,7-TRIMETHYLBICYCLO[2.2.1]HEPTANE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:98 , VAL A:113 , TRP A:121 , ARG A:125 , ILE A:179 , ALA A:298 , GLY A:299 , THR A:302 , THR A:306 , GLN A:357 , LEU A:362 , VAL A:367 , HIS A:369 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , ALA A:442 , HOH A:847 , HOH A:872binding site for residue HEM A 501
2AC2SOFTWAREPHE A:188 , GLU A:194 , MET A:198 , PHE A:202 , TYR A:244 , PHE A:296 , HOH A:604 , LYS B:384binding site for residue CM5 A 503
3AC3SOFTWAREMET A:46 , ASP A:47 , ARG A:48 , HOH A:704binding site for residue CM5 A 504
4AC4SOFTWAREILE A:114 , PHE A:115 , PHE A:206 , PHE A:297 , ALA A:298 , LEU A:363 , HOH A:872binding site for residue 82S A 505
5AC5SOFTWAREARG B:98 , VAL B:113 , TRP B:121 , ARG B:125 , LEU B:295 , ALA B:298 , GLY B:299 , THR B:302 , THR B:306 , GLN B:357 , LEU B:362 , VAL B:367 , HIS B:369 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , HOH B:811 , HOH B:839binding site for residue HEM B 501
6AC6SOFTWAREPHE B:223binding site for residue CM5 B 502
7AC7SOFTWARELYS A:384 , PHE B:188 , GLU B:194 , PHE B:195 , MET B:198 , ALA B:243 , TYR B:244 , PHE B:296 , HOH B:756binding site for residue CM5 B 503
8AC8SOFTWARELEU B:43 , ARG B:48 , HOH B:826binding site for residue CM5 B 504
9AC9SOFTWAREILE B:114 , PHE B:115 , PHE B:206 , PHE B:297 , ALA B:298 , THR B:302 , LEU B:363 , HOH B:839binding site for residue 82S B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UAP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UAP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UAP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UAP)

(-) Exons   (0, 0)

(no "Exon" information available for 5UAP)

(-) 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:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uap A  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR 491
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487    


Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uap B  29 KLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPRH 492
                                    38        48        58        68        78        88        98       108       118       128      |139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489   
                                                                                                                                    135|                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                     137
   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 5UAP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UAP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UAP)

(-) 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
    82S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CM5  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5uap)
 
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
  5uap
    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
 
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 4rrt 4zv8 5uda 5uec 5ufg

(-) Related Entries Specified in the PDB File

5uda 5uec