3R1B

Open crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene

Structural Biology Knowledgebase: 3R1B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3R1B

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 223692.31

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B4 A, B, C, D 476 Oryctolagus cuniculus EC#: 1.14.14.1 IUBMB
Mutation: E21A, ΔF3, ΔS4, ΔL5, ΔL6, ΔL7, ΔL8, ΔL9, ΔA10, ΔF11, ΔL12, ΔA14, ΔG14, ΔL15, ΔL16, ΔL17, ΔL18, ΔL19, ΔF20, ΔR21, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, H226Y
Gene Name(s): CYP2B4

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B, C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CM5
Query on CM5

A, B, D 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL- BETA-D-GLUCOPYRANOSIDE; CYMAL-5 (Synonym)
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A, B, C, D SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TB2
Query on TB2

A, B, C, D (4-tert-butylphenyl)acetaldehyde
C12 H16 O
VMLYBYNXKMHLIJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.242
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 193.92 α = 90.00
b = 153.69 β = 122.22
c = 129.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-09
  • Released Date: 2011-05-11
  • Deposition author(s): Gay, S.C., Zhang, H., Stout, C.D., Hollenberg, P.F., Halpert, J.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4