3CAV

Crystal structure of 5beta-reductase (AKR1D1) in complex with NADP+ and 5beta-pregnan-3,20-dione

Structural Biology Knowledgebase: 3CAV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3CAV

Classification: OXIDOREDUCTASE

Total Structure Weight: 77442.86

Macromolecule Entities
Molecule Chains Length Organism Details
3-oxo-5-beta-steroid 4-dehydrogenase A, B 326 Homo sapiens EC#: 1.3.1.3 IUBMB
Gene Name(s): AKR1D1 Gene View SRD5B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A, B NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CI2
Query on CI2

A, B (5BETA)-PREGNANE-3,20-DIONE
C21 H32 O2
XMRPGKVKISIQBV-XWOJZHJZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.207
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.65 α = 90.00
b = 111.27 β = 90.00
c = 130.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-02-20
  • Released Date: 2008-07-29
  • Deposition author(s): Faucher, F., Cantin, L., Breton, R.

Revision History

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