2D2O Hydrolase date Sep 13, 2005
title Structure Of A Complex Of Thermoactinomyces Vulgaris R-47 Al Amylase 2 With Maltohexaose Demonstrates The Important Role Aromatic Residues At The Reducing End Of The Substrate Bind
authors A.Ohtaki, M.Mizuno, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori
compound source
Molecule: Neopullulanase 2
Chain: A, B
Synonym: Alpha-Amylase II, Tva II
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermoactinomyces Vulgaris
Organism_taxid: 2026
Strain: R-47
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.217
length a length b length c angle alpha angle beta angle gamma
113.690 118.710 112.380 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, GLC enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceStructure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft., Ohtaki A, Mizuno M, Yoshida H, Tonozuka T, Sakano Y, Kamitori S, Carbohydr Res. 2006 Jun 12;341(8):1041-6. Epub 2006 Mar 27. PMID:16564038
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (2d2o.pdb1.gz) 209 Kb
  • LPC: Ligand-Protein Contacts for 2D2O
  • CSU: Contacts of Structural Units for 2D2O
  • Likely Quarternary Molecular Structure file(s) for 2D2O
  • Structure Factors (868 Kb)
  • Retrieve 2D2O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D2O from S2C, [Save to disk]
  • Re-refined 2d2o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D2O 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 2D2O
  • 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 2D2O, from MSDmotif at EBI
  • Fold representative 2d2o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d2o_A] [2d2o_B] [2d2o]
  • SWISS-PROT database: [Q08751]
  • Domain organization of [NEPU2_THEVU] by SWISSPFAM
  • Domain found in 2D2O: [Aamy ] by SMART
  • Other resources with information on 2D2O
  • Community annotation for 2D2O 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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