2D2I Oxidoreductase date Sep 09, 2005
title Crystal Structure Of Nadp-Dependent Glyceraldehyde-3- Phosphate Dehydrogenase From Synechococcus Sp. Complexed With Nadp+
authors T.Kitatani, Y.Nakamura, K.Wada, T.Kinoshita, M.Tamoi, S.Shigeoka, T.Tada
compound source
Molecule: Glyceraldehyde 3-Phosphate Dehydrogenase
Chain: A, B, O, P, Q, R
Ec: 1.2.1.13
Engineered: Yes
Organism_scientific: Synechococcus Sp.
Organism_taxid: 1131
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: C 1 2 1
R_factor 0.191 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
150.006 79.588 206.155 90.00 101.31 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAP, SO4 enzyme Oxidoreductase E.C.1.2.1.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, Q, O, R, P, B


Primary referenceStructure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP., Kitatani T, Nakamura Y, Wada K, Kinoshita T, Tamoi M, Shigeoka S, Tada T, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt, 4):315-9. Epub 2006 Mar 10. PMID:16582475
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (340 Kb) [Save to disk]
  • Biological Unit Coordinates (2d2i.pdb1.gz) 226 Kb
  • Biological Unit Coordinates (2d2i.pdb2.gz) 222 Kb
  • LPC: Ligand-Protein Contacts for 2D2I
  • CSU: Contacts of Structural Units for 2D2I
  • Likely Quarternary Molecular Structure file(s) for 2D2I
  • Structure Factors (575 Kb)
  • Retrieve 2D2I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D2I from S2C, [Save to disk]
  • Re-refined 2d2i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D2I 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 2D2I
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2D2I, from MSDmotif at EBI
  • Fold representative 2d2i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d2i_P] [2d2i_B] [2d2i_Q] [2d2i_A] [2d2i_O] [2d2i] [2d2i_R]
  • SWISS-PROT database: [Q55245]
  • Domain organization of [Q55245_SYNSP] by SWISSPFAM
  • Domain found in 2D2I: [Gp_dh_N ] by SMART
  • Other resources with information on 2D2I
  • Community annotation for 2D2I 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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