3S42

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site

Structural Biology Knowledgebase: 3S42 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.144

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S42

Classification: LYASE

Total Structure Weight: 61069.59

Macromolecule Entities
Molecule Chains Length Organism Details
3-dehydroquinate dehydratase A, B 276 Salmonella enterica EC#: 4.2.1.10 IUBMB
Gene Name(s): aroD STM1358
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MLA
Query on MLA

A, B MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID (Synonym)
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

B IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BO3
Query on BO3

A BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.144
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 36.56 α = 90.00
b = 72.57 β = 90.00
c = 171.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-18
  • Released Date: 2011-06-01
  • Deposition author(s): Light, S.H., Minasov, G., Duban, M.-E., Halavaty, A.S., Krishna, S.N., Shuvalova, L., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • 2015-04-29
    Type: Non-polymer description | Details: --
  • 2014-10-29
    Type: Entry authorship | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4