3PEF

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.156

Literature

Macromolecules
Sequence Display for 3PEF

Classification: OXIDOREDUCTASE

Total Structure Weight: 246583.67

Macromolecule Entities
Molecule Chains Length Organism Details
6-phosphogluconate dehydrogenase, NAD-binding A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 287 Geobacter metallireducens Mutation: M1S, I285Y
Gene Name(s): ghr Gmet_3011
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A, B, C, D, E, F, G, H 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)
PEG
Query on PEG

A, D, E, G, H DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, E GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.156
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 75.97 α = 82.15
b = 79.14 β = 88.80
c = 95.47 γ = 87.66

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-26
  • Released Date: 2011-12-07
  • Deposition author(s): Zhang, Y., Garavito, R.M.

Revision History

  • 2016-06-01
    Type: Citation | Details: Citation update