5J23

Crystal structure of NADP-dependent 2-hydroxyacid dehydrogenase from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose

Structural Biology Knowledgebase: 5J23 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.169
  • R-Value Work: 0.146

Literature

Macromolecules
Sequence Display for 5J23

Classification: OXIDOREDUCTASE

Total Structure Weight: 140416.47

Macromolecule Entities
Molecule Chains Length Organism Details
2-hydroxyacid dehydrogenase A, B, C, D 323 Sinorhizobium meliloti Gene Name(s): SMc04462
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A2R
Query on A2R

A, B, C, D [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)- 3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN- 2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN- 2-YL]METHYL DIHYDROGEN DIPHOSPHATE
C15 H24 N5 O17 P3
ICNHOLCERMYLRZ-KEOHHSTQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, C ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 175.82 α = 90.00
b = 175.82 β = 90.00
c = 136.84 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-03-29
  • Released Date: 2016-04-13
  • Deposition author(s): Shabalin, I.G., Gasiorowska, O.A., Handing, K.B., Bonanno, J., Kutner, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

No revisions since initial release