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1.78 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Quinate

Structural Biology Knowledgebase: 4GUI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GUI

Classification: LYASE

Total Structure Weight: 55996.14

Macromolecule Entities
Molecule Chains Length Organism Details
3-dehydroquinate dehydratase A, B 255 Salmonella enterica EC#: 4.2.1.10 IUBMB
Gene Name(s): aroD STM1358

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

A, B (1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid
Quinic acid (Synonym)
C7 H12 O6
AAWZDTNXLSGCEK-WYWMIBKRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
QIC N/A in BindingDB
N/A in BindingMoad
Kd: 230000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.159
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 48.67 α = 90.00
b = 74.43 β = 100.57
c = 63.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-29
  • Released Date: 2012-09-12
  • Deposition author(s): Light, S.H., Minasov, G., Duban, M.-E., Shuvalova, L., Kwon, K., Lavie, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • 2014-03-05
    Type: Citation | Details: Citation update