4MMW

Crystal structure of D-glucarate dehydratase from Agrobacterium tumefaciens complexed with magnesium, L-Xylarohydroxamate and L-Lyxarohydroxamate

Structural Biology Knowledgebase: 4MMW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4MMW

Classification: ISOMERASE

Total Structure Weight: 92412.83

Macromolecule Entities
Molecule Chains Length Organism Details
Isomerase/lactonizing enzyme A, B 405 Agrobacterium fabrum Gene Name(s): Atu3453

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

A, B (2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)- 5-OXOPENTANOIC ACID
C5 H9 N O7
DMGBHBFPSRKPBV-ZVHKOUPVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XYH
Query on XYH

A, B XYLAROHYDROXAMATE
C5 H8 N O7
DMGBHBFPSRKPBV-XZIMBLGRSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.65 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.170
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 118.10 α = 90.00
b = 118.10 β = 90.00
c = 133.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-09
  • Released Date: 2013-09-18
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Gerlt, J.A., Almo, S.C.

Revision History

No revisions since initial release