1VFU Crystal structure of Thermoactinomyces vulgaris R-47 amylase 2/gamma-cyclodextrin complex date
authors Ohtaki, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.
compound source
R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.10
ligand CA, GLC enzyme
A, B

Primary referenceComplex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism., Ohtaki A, Mizuno M, Tonozuka T, Sakano Y, Kamitori S, J Biol Chem 2004 Jul 23;279(30):31033-40. Epub 2004 May 11. PMID:15138257
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (204 Kb) [Save to disk]
  • Biological Unit Coordinates (1vfu.pdb1.gz) 99 Kb
  • Biological Unit Coordinates (1vfu.pdb2.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 1VFU
  • CSU: Contacts of Structural Units for 1VFU
  • Likely Quarternary Molecular Structure file(s) for 1VFU
  • Structure Factors (233 Kb)
  • Retrieve 1VFU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VFU from S2C, [Save to disk]
  • Re-refined 1vfu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VFU 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 1VFU
  • 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 1VFU, from MSDmotif at EBI
  • Fold representative 1vfu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vfu_B] [1vfu] [1vfu_A]
  • SWISS-PROT database: [Q08751]
  • Domain organization of [NEPU2_THEVU] by SWISSPFAM
  • Domain found in 1VFU: [Aamy ] by SMART
  • Other resources with information on 1VFU
  • Community annotation for 1VFU 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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