1WDR Hydrolase date May 17, 2004
title The Role Of An Inner Loop In The Catalytic Mechanism Of Soyb Amylase
authors Y.N.Kang, M.Adachi, S.Utsumi, B.Mikami
compound source
Molecule: Beta-Amylase
Chain: A
Synonym: 1,4-Alpha-D-Glucan Maltohydrolase
Ec: 3.2.1.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Glycine Max
Organism_common: Soybean
Organism_taxid: 3847
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm105
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkk233-2
symmetry Space Group: P 31 2 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.128 85.128 143.598 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.35 Å
ligand CME, GLC, SO4 enzyme Hydrolase E.C.3.2.1.2 BRENDA
related structures by homologous chain: 1V3H, 1WDQ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism., Kang YN, Tanabe A, Adachi M, Utsumi S, Mikami B, Biochemistry. 2005 Apr 5;44(13):5106-16. PMID:15794648
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (206 Kb) [Save to disk]
  • Biological Unit Coordinates (1wdr.pdb1.gz) 196 Kb
  • LPC: Ligand-Protein Contacts for 1WDR
  • CSU: Contacts of Structural Units for 1WDR
  • Likely Quarternary Molecular Structure file(s) for 1WDR
  • Structure Factors (1119 Kb)
  • Retrieve 1WDR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WDR from S2C, [Save to disk]
  • Re-refined 1wdr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1WDR 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 1WDR
  • 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 1WDR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wdr] [1wdr_A]
  • SWISS-PROT database: [P10538]
  • Domain organization of [AMYB_SOYBN] by SWISSPFAM
  • Other resources with information on 1WDR
  • Community annotation for 1WDR 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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