2YID

CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE

Structural Biology Knowledgebase: 2YID SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YID

Classification: LYASE

Total Structure Weight: 391032.78

Macromolecule Entities
Molecule Chains Length Organism Details
2-OXOGLUTARATE DECARBOXYLASE A, B, C, D 868 Mycobacterium smegmatis EC#: 4.1.1.71 IUBMB
Fragment: RESIDUES 361-1227
Gene Name(s): kgd sucA MSMEG_5049 MSMEI_4922
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TD7
Query on TD7

A, B, C, D (4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]- 5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)- 4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid
C16 H24 N4 O10 P2 S
VGWJMSNWDAXPBE-FOWTUZBSSA-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: 2.25 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.192
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 79.84 α = 99.23
b = 82.29 β = 99.03
c = 163.48 γ = 100.63

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-11
  • Released Date: 2011-06-15
  • Deposition author(s): Wagner, T., Bellinzoni, M., Wehenkel, A.M., O'Hare, H.M., Alzari, P.M.

Revision History

  • 2011-10-12
    Type: Citation | Details: JRNL
  • 2011-10-12
    Type: Version format compliance | Details: REMARK 4