5BQF

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.139

Literature

Macromolecules
Sequence Display for 5BQF

Classification: OXIDOREDUCTASE

Total Structure Weight: 37091.18

Macromolecule Entities
Molecule Chains Length Organism Details
NADP-dependent 2-hydroxyacid dehydrogenase A 322 Rhizobium etli Gene Name(s): RHE_CH00179
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A 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)
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TLA
Query on TLA

A L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A 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 = 65.69 α = 90.00
b = 65.69 β = 90.00
c = 151.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-05-29
  • Released Date: 2015-06-17
  • Deposition author(s): Langner, K.M., Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Stead, M., Hillerich, B.S., Chowdhury, S., Hammonds, J., Zimmerman, M.D., Al Obaidi, N., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

  • Version 1_0: 2015-06-17

    Type: Initial release

  • Version 1_1: 2017-09-20

    Type: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy