4C3X

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1

Structural Biology Knowledgebase: 4C3X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4C3X

Classification: OXIDOREDUCTASE

Total Structure Weight: 456559.72

Macromolecule Entities
Molecule Chains Length Organism Details
3-KETOSTEROID DEHYDROGENASE A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 530 Rhodococcus erythropolis EC#: 1.3.99.4 IUBMB
Gene Name(s): kstD1 XU06_24615

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, B, C, D, E, F, G, H FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A, B, C, D, E, F, G, H SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A, B, C, D, E, F, G, H TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D, E, F, G, H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, C, E, G SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.177
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 107.39 α = 90.00
b = 131.63 β = 90.00
c = 363.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-28
  • Released Date: 2013-11-06
  • Deposition author(s): Rohman, A., van Oosterwijk, N., Thunnissen, A.M.W.H., Dijkstra, B.W.

Revision History

  • 2013-12-25
    Type: Citation | Details: JRNL