5VG6

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 5VG6

Classification: OXIDOREDUCTASE

Total Structure Weight: 381025.75

Macromolecule Entities
Molecule Chains Length Organism Details
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 341 Xanthobacter autotrophicus Gene Name(s): Xaut_2571
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H, I, J NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A, B, C, D, E, F, I, J 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.200
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 132.51 α = 90.00
b = 311.04 β = 90.00
c = 98.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-10
  • Released Date: 2017-04-26
  • Deposition author(s): Lipowska, J., Shabalin, I.G., Kutner, J., Gasiorowska, O.A., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

No revisions since initial release