1UD8 Hydrolase date Apr 28, 2003
title Crystal Structure Of Amyk38 With Lithium Ion
authors T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki
compound source
Molecule: Amylase
Chain: A
Fragment: Residues 1-480
Synonym: Alpha-Amylase
Ec: 3.2.1.1
Engineered: Yes
Organism_scientific: Bacillus Sp. Ksm-K38
Organism_taxid: 129736
Expression_system: Bacillus Subtilis
Expression_system_taxid: 1423
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phsp64
symmetry Space Group: P 2 3
R_factor 0.205 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.553 132.553 132.553 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.88 Å
ligand NA enzyme Hydrolase E.C.3.2.1.1 BRENDA
related structures by homologous chain: 1UD5
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites., Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K, J Biol Chem 2003 Apr 28;. PMID:12719434
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (1ud8.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 1UD8
  • CSU: Contacts of Structural Units for 1UD8
  • Likely Quarternary Molecular Structure file(s) for 1UD8
  • Retrieve 1UD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UD8 from S2C, [Save to disk]
  • View 1UD8 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 1UD8
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1UD8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ud8a2, region A:1-390 [Jmol] [rasmolscript] [script source]
        - Domain d1ud8a1, region A:391-480 [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: [1ud8_A] [1ud8]
  • SWISS-PROT database: [Q93I48]
  • Domain organization of [Q93I48_9BACI] by SWISSPFAM
  • Domain found in 1UD8: [Aamy ] by SMART
  • Other resources with information on 1UD8
  • Community annotation for 1UD8 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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