3DC2 Oxidoreductase date Jun 03, 2008
title Crystal Structure Of Serine Bound D-3-Phosphoglycerate Dehyd From Mycobacterium Tuberculosis
authors S.Dey, J.C.Sacchettini
compound source
Molecule: D-3-Phosphoglycerate Dehydrogenase
Chain: A, B
Synonym: Pgdh
Ec: 1.1.1.95
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Strain: H37rv
Gene: Sera1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30b
symmetry Space Group: P 65 2 2
R_factor 0.222 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.192 165.192 218.894 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand SER, TLA enzyme Oxidoreductase E.C.1.1.1.95 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase., Dey S, Burton RL, Grant GA, Sacchettini JC, Biochemistry. 2008 Aug 12;47(32):8271-82. Epub 2008 Jul 16. PMID:18627175
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (162 Kb) [Save to disk]
  • Biological Unit Coordinates (3dc2.pdb1.gz) 305 Kb
  • LPC: Ligand-Protein Contacts for 3DC2
  • CSU: Contacts of Structural Units for 3DC2
  • Likely Quarternary Molecular Structure file(s) for 3DC2
  • Structure Factors (378 Kb)
  • Retrieve 3DC2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DC2 from S2C, [Save to disk]
  • Re-refined 3dc2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DC2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3DC2
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DC2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m3dc2, region C:115-226 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dc2_A] [3dc2_B] [3dc2]
  • SWISS-PROT database: [P0A544]
  • Domain organization of [SERA_MYCTU] by SWISSPFAM
  • Other resources with information on 3DC2
  • Community annotation for 3DC2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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