2YOO

Cholest-4-en-3-one bound structure of CYP142 from Mycobacterium smegmatis

Structural Biology Knowledgebase: 2YOO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YOO

Classification: OXIDOREDUCTASE

Total Structure Weight: 187150.63

Macromolecule Entities
Molecule Chains Length Organism Details
P450 HEME-THIOLATE PROTEIN A, B, C, D 407 Mycobacterium smegmatis Details: 6XHIS TAG ENGINEERED AT C-TERMINUS
Gene Name(s): MSMEG_5918

Small Molecules
Ligands 3 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)
K2B
Query on K2B

A, B, C, D (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
C27 H44 O
NYOXRYYXRWJDKP-GYKMGIIDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
K2B N/A in BindingDB
Kd: 520 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.165
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.68 α = 90.00
b = 106.21 β = 90.67
c = 126.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-25
  • Released Date: 2013-02-27
  • Deposition author(s): Garcia-Fernandez, E., Frank, D.J., Galan, B., Kells, P.M., Podust, L.M., Garcia, J.L., Ortiz de Montellano, P.R.

Revision History

  • 2013-08-14
    Type: Citation | Details: JRNL
  • 2013-05-01
    Type: Citation | Details: JRNL