2Q9F

Crystal structure of human cytochrome P450 46A1 in complex with cholesterol-3-sulphate

Structural Biology Knowledgebase: 2Q9F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2Q9F

Classification: OXIDOREDUCTASE

Total Structure Weight: 53856.45

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 46A1 A 456 Homo sapiens EC#: 1.14.14.25 IUBMB
Fragment: RESIDUES 51-500
Gene Name(s): CYP46A1 Gene View CYP46
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
C3S
Query on C3S

A CHOLEST-5-EN-3-YL HYDROGEN SULFATE
CHOLESTEROL-SULFATE (Synonym)
C27 H46 O4 S
BHYOQNUELFTYRT-DPAQBDIFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C3S N/A in BindingDB
Kd: 7 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.183
  • Space Group: I 41 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.85 α = 90.00
b = 121.85 β = 90.00
c = 144.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-12
  • Released Date: 2008-06-17
  • Deposition author(s): White, M.A., Mast, N.V., Johnson, E.F., Stout, C.D., Pikuleva, I.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update