1NVF

Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, ADP and carbaphosphonate

Structural Biology Knowledgebase: 1NVF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 1NVF

Classification: lyase

Total Structure Weight: 131330.94

Macromolecule Entities
Molecule Chains Length Organism Details
3-DEHYDROQUINATE SYNTHASE A, B, C 393 Aspergillus nidulans EC#: 4.2.3.4 IUBMB
Gene Name(s): aromA aroA aroM AN0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CRB
Query on CRB

A, B, C [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)- 1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
CARBAPHOSPHONATE (Synonym)
C8 H15 O8 P
BKLICLLAHMTUPK-UNGCPHIMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.184
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 206.50 α = 90.00
b = 136.40 β = 90.00
c = 40.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-03
  • Released Date: 2003-03-18
  • Deposition author(s): Nichols, C.E., Ren, J., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4