3ZHV

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)

Structural Biology Knowledgebase: 3ZHV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZHV

Classification: OXIDOREDUCTASE

Total Structure Weight: 390804.66

Macromolecule Entities
Molecule Chains Length Organism Details
MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME A, B, C, D 868 Mycobacterium smegmatis EC#: 1.2.4.2 IUBMB 2.2.1.5 IUBMB 2.3.1.61 IUBMB 4.1.1.71 IUBMB
Fragment: SUCA-LIKE CATALYTIC DOMAIN, RESIDUES 361-1227
Gene Name(s): kgd sucA MSMEG_5049 MSMEI_4922

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

A, B, C, D 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]- 4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol- 3-ium-5-yl]ethyl phosphono hydrogen phosphate
C14 H23 N4 O8 P2 S
WHPLAPKWYDKPQH-VIFPVBQESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.203
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.46 α = 99.68
b = 83.70 β = 98.87
c = 160.33 γ = 100.63

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-24
  • Released Date: 2013-11-13
  • Deposition author(s): Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.

Revision History

  • 2014-01-29
    Type: Citation | Details: JRNL