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 :  STRUCTURE OF P450 2B4 F202W MUTANT (CYMAL-5)
 
Authors :  H. -H. Jang, J. R. Halpert, M. B. Shah
Date :  18 Mar 16  (Deposition) - 08 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Monooxygenase, Membrane Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shah, H. H. Jang, P. R. Wilderman, D. Lee, S. Li, Q. Zhang, C. D. Stout, J. R. Halpert
Effect Of Detergent Binding On Cytochrome P450 2B4 Structur As Analyzed By X-Ray Crystallography And Deuterium-Exchange Mass Spectrometry.
Biophys. Chem. V. 216 1 2016
PubMed-ID: 27280734  |  Reference-DOI: 10.1016/J.BPC.2016.05.007

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B4
    Chains: A, B
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK
    Expression System Strain: TOPP3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-491
    Gene: CYP2B4
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: CYPIIB4,CYTOCHROME P450 ISOZYME 2,CYTOCHROME P450 LM2, CYTOCHROME P450 TYPE B0,CYTOCHROME P450 TYPE B1

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CM54Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CM52Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CM52Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , ILE A:179 , ALA A:298 , GLY A:299 , THR A:302 , THR A:303 , THR A:306 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , ALA A:442binding site for residue HEM A 501
2AC2SOFTWARELYS A:186 , PHE A:188 , LEU A:198 , PHE A:244 , LYS A:251 , ASP A:467binding site for residue CM5 A 502
3AC3SOFTWARELEU A:44 , MET A:46 , ASP A:47 , GLY A:50 , VAL A:216 , HOH A:648 , HOH A:679 , HOH A:721binding site for residue CM5 A 503
4AC4SOFTWAREARG B:98 , ILE B:114 , TRP B:121 , ARG B:125 , ALA B:298 , GLY B:299 , THR B:302 , THR B:303 , THR B:306 , ILE B:363 , VAL B:367 , HIS B:369 , LEU B:392 , PRO B:428 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , HOH B:636binding site for residue HEM B 501
5AC5SOFTWAREPHE B:188 , PHE B:195 , LEU B:198 , PHE B:244 , PHE B:296 , ASP B:467 , HOH B:601 , HOH B:668binding site for residue CM5 B 502
6AC6SOFTWARELEU B:43 , MET B:46 , ASP B:47 , GLY B:50binding site for residue CM5 B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IUZ)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh...hhhhee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....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
                 5iuz A  29 KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLWFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTFIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPRESGVGNVPPSYQIRFLARH 492
                                    38        48        58        68        78        88        98       108       118       128     ||143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483         
                                                                                                                                   134|                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                    140                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...hhhhee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeee.hhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iuz B  29 KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDFGMGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLWFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTFIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPRESGVGNVPPSYQIRFLARH 492
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488
   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 5IUZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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
    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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5iuz)
 
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
  5iuz
    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
  CP2B4_RABIT | P00178
    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)
  1.14.14.1
    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
  CP2B4_RABIT | P00178
    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
        CP2B4_RABIT | P00178: 1po5 1suo 2bdm 2q6n 3g5n 3g93 3kw4 3me6 3mvr 3r1a 3r1b 3tk3 3tmz 3uas 4h1n 4jlt 4mgj 5em4 5iut

(-) Related Entries Specified in the PDB File

1po5 CYTOCHROME P450 2B4 IN A LIGAND-FREE OPEN CONFORMATION
1suo CYTOCHROME P450 2B4 COMPLEXED WITH 4-(4-CHLOROPHENYL) IMIDAZOLE
2bdm CYTOCHROME P450 2B4 COMPLEXED WITH BIFONAZOLE
2q6n CYTOCHROME P450 2B4 COMPLEXED WITH 1-(4-CHLOROPHENYL) IMIDAZOLE
3g5n CYTOCHROME P450 2B4 COMPLEXED WITH 1-BIPHENYL-4-METHYL-1H- IMIDAZOLE (TRIPLE LIGAND OCCUPANCY)
3g93 CYTOCHROME P450 2B4 COMPLEXED WITH 1-BIPHENYL-4-METHYL-1H- IMIDAZOLE (SINGLE LIGAND OCCUPANCY)
3kw4 CYTOCHROME P450 2B4 COMPLEXED WITH TICLOPIDINE
3me6 CYTOCHROME P450 2B4 COMPLEXED WITH CLOPIDOGREL
3mvr CYTOCHROME P450 2B4 IN A LIGAND-FREE CLOSED CONFORMATION
3r1a CYTOCHROME P450 2B4 COMPLEXED WITH TERT- BUTYLPHENYLACETYLENE (CLOSED CONFORMATION)
3r1b CYTOCHROME P450 2B4 COMPLEXED WITH TERT- BUTYLPHENYLACETYLENE (OPEN CONFORMATION)
3tk3 CYTOCHROME P450 2B4 L437A MUTANT COMPLEXED WITH 4-(4- CHLOROPHENYL) IMIDAZOLE
3tmz CYTOCHROME P450 2B4 COMPLEXED WITH AMLODIPINE
3uas CYTOCHROME P450 2B4 COMPLEXED WITH 9-ETHYNYLPHENANTHRENE
4h1n CYTOCHROME P450 2B4 F297A MUTANT COMPLEXED WITH CLOPIDOGREL
4jlt CYTOCHROME P450 2B4 COMPLEXED WITH PAROXETINE
5em4 P450 2B4 F244W IN A LIGAND FREE CONFORMATION
5iut