5J23

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Shabalin, I.G.Gasiorowska, O.A.Handing, K.B.Bonanno, J.Kutner, J.Almo, S.C.Minor, W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-hydroxyacid dehydrogenase
A, B, C, D
323Rhizobium meliloti (strain 1021)N/A
Find proteins for Q92LZ4 (Rhizobium meliloti (strain 1021))
Go to UniProtKB:  Q92LZ4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2R
Query on A2R

Download SDF File 
Download CCD File 
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 Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 175.822α = 90.00
b = 175.822β = 90.00
c = 136.839γ = 120.00
Software Package:
Software NamePurpose
MD2data collection
HKL-3000phasing
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references, Derived calculations
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence