4APY

Ethylene glycol-bound form of P450 CYP125A3 from Mycobacterium smegmatis

Structural Biology Knowledgebase: 4APY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4APY

Classification: OXIDOREDUCTASE

Total Structure Weight: 49321.98

Macromolecule Entities
Molecule Chains Length Organism Details
P450 HEME-THIOLATE PROTEIN A 433 Mycobacterium smegmatis Gene Name(s): cyp125 MSMEI_5834

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)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.164
  • Space Group: I 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.19 α = 90.00
b = 108.19 β = 90.00
c = 120.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-09
  • Released Date: 2013-02-27
  • Deposition author(s): Frank, D.J., Garcia Fernandez, E., Kells, P.M., Garcia Lopez, J.L., Podust, L.M., Ortiz de Montellano, P.R.

Revision History

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