1DYP Hydrolase date Feb 04, 2000
title 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase
authors G.Michel, L.Chantalat, O.Dideberg
compound source
Molecule: Kappa-Carrageenase
Chain: A
Fragment: Catalytic Domain
Engineered: Yes
Mutation: Yes
Other_details: Complexed With Cadmium Chloride
Organism_scientific: Pseudoalteromonas Carrageenovora
Organism_taxid: 227
Plasmid: Pet20b
Gene: Cgka
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_plasmid: Pet20b
Other_details: Processed Protein, His-Tag, Selemethionyl Protein
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.193
length a length b length c angle alpha angle beta angle gamma
56.408 61.120 75.523 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.54 Å
ligand CD, CL, MSE enzyme Hydrolase E.C. BRENDA

Primary referenceThe kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases., Michel G, Chantalat L, Duee E, Barbeyron T, Henrissat B, Kloareg B, Dideberg O, Structure. 2001 Jun;9(6):513-25. PMID:11435116
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1dyp.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 1DYP
  • CSU: Contacts of Structural Units for 1DYP
  • Likely Quarternary Molecular Structure file(s) for 1DYP
  • Retrieve 1DYP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DYP from S2C, [Save to disk]
  • View 1DYP 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 1DYP
  • 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 1DYP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dypa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1dyp 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: [1dyp] [1dyp_A]
  • SWISS-PROT database: [P43478]
  • Domain organization of [CGKA_ALTCA] by SWISSPFAM
  • Other resources with information on 1DYP
  • Community annotation for 1DYP 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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