2BDM

Structure of Cytochrome P450 2B4 with Bound Bifonazole

Structural Biology Knowledgebase: 2BDM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BDM

Classification: OXIDOREDUCTASE

Total Structure Weight: 57695.79

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B4 A 476 Oryctolagus cuniculus EC#: 1.14.14.1 IUBMB
Fragment: residues 28-491
Mutation: E21A, ΔF3, ΔS4, ΔL5, ΔL6, ΔL7, ΔL8, ΔL9, ΔA10, ΔF11, ΔL12, ΔA13, ΔG14, ΔL15, ΔL16, ΔL17, ΔL18, ΔL19, ΔF20, ΔR21, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, H226Y
Gene Name(s): CYP2B4

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

A 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 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)
TMI
Query on TMI

A 1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE
BIFONAZOLE (Synonym)
C22 H18 N2
OCAPBUJLXMYKEJ-QFIPXVFZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TMI N/A in BindingDB
IC50: 900 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.196
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 203.21 α = 90.00
b = 203.21 β = 90.00
c = 103.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-20
  • Released Date: 2005-12-27
  • Deposition author(s): Zhao, Y., White, M.A., Muralidhara, B.K., Sun, L., Halpert, J.R., Stout, C.D.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4