1KY5 Hydrolase date Feb 03, 2002
title D244e Mutant S-Adenosylhomocysteine Hydrolase Refined With Noncrystallographic Restraints
authors Y.Takata, F.Takusagawa
compound source
Molecule: S-Adenosylhomocysteine Hydrolase
Chain: A, B, C, D
Synonym: Adenosylhomocysteinase, Adohcyase
Engineered: Yes
Mutation: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.215 R_Free 0.293
length a length b length c angle alpha angle beta angle gamma
91.000 223.000 91.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ADY, NAI enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1A7A, 1B3R
A, D, C, B

Primary referenceCatalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190., Takata Y, Yamada T, Huang Y, Komoto J, Gomi T, Ogawa H, Fujioka M, Takusagawa F, J Biol Chem 2002 Jun 21;277(25):22670-6. Epub 2002 Apr 1. PMID:11927587
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk]
  • Biological Unit Coordinates (1ky5.pdb1.gz) 275 Kb
  • LPC: Ligand-Protein Contacts for 1KY5
  • CSU: Contacts of Structural Units for 1KY5
  • Likely Quarternary Molecular Structure file(s) for 1KY5
  • Retrieve 1KY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KY5 from S2C, [Save to disk]
  • View 1KY5 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 1KY5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KY5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ky5a1, region A:190-352 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5a2, region A:2-189,A:353-431 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5b2, region B:1002-1189,B:1353-1431 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5b1, region B:1190-1352 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5c2, region C:2002-2189,C:2353-2431 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5c1, region C:2190-2352 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5d2, region D:3002-3189,D:3353-3431 [Jmol] [rasmolscript] [script source]
        - Domain d1ky5d1, region D:3190-3352 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ky5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1ky5_D] [1ky5_A] [1ky5_B] [1ky5_C] [1ky5]
  • SWISS-PROT database: [P10760]
  • Domain organization of [SAHH_RAT] by SWISSPFAM
  • Domains found in 1KY5: [AdoHcyase] [AdoHcyase_NAD ] by SMART
  • Other resources with information on 1KY5
  • Community annotation for 1KY5 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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