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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Lipowska, J.Shabalin, I.G.Almo, S.C.Minor, W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
A, B, C, D, E, F, G, H, I, J
341Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)Mutation(s): 0 
Find proteins for A7IIH0 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2))
Go to UniProtKB:  A7IIH0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download SDF File 
Download CCD File 
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 Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B, C, D, E, F, I, J
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 132.514α = 90.00
b = 311.036β = 90.00
c = 98.977γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
HKL-3000data collection
PDB_EXTRACTdata extraction
HKL-3000phasing
SCALEPACKdata scaling
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States--

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Refinement description