1BVZ Hydrolase date Sep 22, 1998
title Alpha-Amylase II (Tvaii) From Thermoactinomyces Vulgaris R-4
authors S.Kamitori, S.Kondo, K.Okuyama, T.Yokota, Y.Shimura, T.Tonozuka, Y
compound source
Molecule: Protein (Alpha-Amylase II)
Chain: A, B
Fragment: N,A,B.C
Ec: 3.2.1.135
Engineered: Yes
 Organism_scientific: Thermoactinomyces Vulgaris
Organism_taxid: 2026
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.600 117.900 114.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand
enzyme Hydrolase E.C.3.2.1.135 BRENDA
related structures by homologous chain: 1VFO, 1WZK
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution., Kamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, Sakano Y, J Mol Biol 1999 Apr 16;287(5):907-21. PMID:10222200
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (1bvz.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (1bvz.pdb2.gz) 102 Kb
  • CSU: Contacts of Structural Units for 1BVZ
  • Likely Quarternary Molecular Structure file(s) for 1BVZ
  • Structure Factors (541 Kb)
  • Retrieve 1BVZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BVZ from S2C, [Save to disk]
  • Re-refined 1bvz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1BVZ 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 1BVZ
  • 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 1BVZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bvza1, region A:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1bvza3, region A:121-502 [Jmol] [rasmolscript] [script source]
        - Domain d1bvza2, region A:503-585 [Jmol] [rasmolscript] [script source]
        - Domain d1bvzb1, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1bvzb3, region B:121-502 [Jmol] [rasmolscript] [script source]
        - Domain d1bvzb2, region B:503-585 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1bvz] [1bvz_A] [1bvz_B]
  • SWISS-PROT database: [Q08751]
  • Domain organization of [NEPU2_THEVU] by SWISSPFAM
  • Domain found in 1BVZ: [Aamy ] by SMART
    • Other resources with information on 1BVZ
  • Community annotation for 1BVZ 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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