2GRU Lyase date Apr 25, 2006
title Crystal Structure Of 2-Deoxy-Scyllo-Inosose Synthase Complex Carbaglucose-6-Phosphate, Nad+ And Co2+
authors E.Nango, T.Kumasaka
compound source
Molecule: 2-Deoxy-Scyllo-Inosose Synthase
Chain: A, B
Ec: 4.2.3.-
Engineered: Yes
Organism_scientific: Bacillus Circulans
Organism_taxid: 1397
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30b
symmetry Space Group: P 1 21 1
R_factor 0.174 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.569 70.108 81.569 90.00 117.61 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CAK, CO, EXO, MPD, NAD, PO4, SO3 enzyme Lyase E.C.4.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+., Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T, Proteins. 2008 Feb 1;70(2):517-27. PMID:17879343
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (2gru.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 2GRU
  • CSU: Contacts of Structural Units for 2GRU
  • Likely Quarternary Molecular Structure file(s) for 2GRU
  • Structure Factors (1129 Kb)
  • Retrieve 2GRU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GRU from S2C, [Save to disk]
  • Re-refined 2gru structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GRU 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 2GRU
  • 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 2GRU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gru] [2gru_B] [2gru_A]
  • SWISS-PROT database: [Q9S5E2]
  • Domain organization of [DOIS_BACCI] by SWISSPFAM
  • Other resources with information on 2GRU
  • Community annotation for 2GRU 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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