5V72

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with citrate

Structural Biology Knowledgebase: 5V72 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.164

Literature

Macromolecules
Sequence Display for 5V72

Classification: OXIDOREDUCTASE

Total Structure Weight: 137626.66

Macromolecule Entities
Molecule Chains Length Organism Details
NADPH-dependent glyoxylate/hydroxypyruvate reductase A, B, C, D 322 Sinorhizobium meliloti EC#: 1.1.1.79 IUBMB 1.1.1.81 IUBMB
Details: His-tag-labelled protein was subjected to limited proteolysis by chymotrypsin immediately prior to crystallization.
Gene Name(s): SMc04462
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

C CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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)
NA
Query on NA

A, B, C, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 63.19 α = 90.00
b = 157.93 β = 110.74
c = 64.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-17
  • Released Date: 2017-03-29
  • Deposition author(s): Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., Matelska, D., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

No revisions since initial release