3EKD

Crystal structure of the A264M heme domain of cytochrome P450 BM3

Structural Biology Knowledgebase: 3EKD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EKD

Classification: OXIDOREDUCTASE

Total Structure Weight: 108887.01

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450(BM-3) A, B 470 Bacillus megaterium EC#: 1.14.14.1 IUBMB
Fragment: heme domain
Mutation: A264M
Gene Name(s): cyp102A1 cyp102

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

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

A PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PAM N/A in BindingDB
Kd: 7400 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.217
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.77 α = 90.00
b = 125.17 β = 90.00
c = 153.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-19
  • Released Date: 2008-12-30
  • Deposition author(s): Toogood, H.S., Leys, D.

Revision History

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