3BUR

Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and TESTOSTERONE. RESOLUTION: 1.62 A.

Structural Biology Knowledgebase: 3BUR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.228

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BUR

Classification: OXIDOREDUCTASE

Total Structure Weight: 77841.09

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
Fragment: AKRD1
Gene Name(s): AKR1D1 Gene View SRD5B1

Small Molecules
Ligands 3 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)
TES
Query on TES

A, B TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B 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 %)
TES N/A in BindingDB
Ki: 14450 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.228
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.82 α = 90.00
b = 109.99 β = 90.00
c = 128.91 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-03
  • Released Date: 2008-04-01
  • Deposition author(s): Di Costanzo, L., Christianson, D.W.

Revision History

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