5V6Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.156
  • R-Value Work: 0.144

Literature

Macromolecules
Sequence Display for 5V6Q

Classification: OXIDOREDUCTASE

Total Structure Weight: 140892.81

Macromolecule Entities
Molecule Chains Length Organism Details
NADPH-dependent glyoxylate/hydroxypyruvate reductase A, B, C, D 323 Sinorhizobium meliloti EC#: 1.1.1.79 IUBMB 1.1.1.81 IUBMB
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
NAP
Query on NAP

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

A, B, C, D MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID (Synonym)
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, 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 = 176.48 α = 90.00
b = 176.48 β = 90.00
c = 135.86 γ = 120.00

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., Miezaniec, A.P., Gasiorowska, O.A., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

  • Version 1_0: 2017-03-29

    Type: Initial release

  • Version 1_1: 2017-09-13

    Type: Author supporting evidence, Refinement description