4GYP

Crystal structure of the heterotetrameric complex of GlucD and GlucDRP from E. coli K-12 MG1655 (EFI TARGET EFI-506058)

Structural Biology Knowledgebase: 4GYP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.149

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GYP

Classification: LYASE / LYASE

Total Structure Weight: 200789.72

Macromolecule Entities
Molecule Chains Length Organism Details
Glucarate dehydratase A, B 446 Escherichia coli EC#: 4.2.1.40 IUBMB
Gene Name(s): gudD ygcX b2787 JW2758
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Glucarate dehydratase-related protein C, D 458 Escherichia coli EC#: 4.2.1 IUBMB
Gene Name(s): gudX ygcY b2788 JW2759
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
P6G
Query on P6G

D HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CIT
Query on CIT

C, D CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, C, D DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.149
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 155.47 α = 90.00
b = 113.02 β = 105.89
c = 128.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-05
  • Released Date: 2012-09-12
  • Deposition author(s): Lukk, T., Ghasempur, S., Imker, H.J., Gerlt, J.A., Nair, S.K., Enzyme Function Initiative (EFI)

Revision History

  • 2012-09-19
    Type: Entry authorship | Details: Update entry authors and title