1KTB Hydrolase date Jan 15, 2002
title The Structure Of Alpha-N-Acetylgalactosaminidase
authors S.C.Garman, L.Hannick, A.Zhu, D.N.Garboczi
compound source
Molecule: Alpha-N-Acetylgalactosaminidase
Chain: A
Ec: 3.2.1.49
Engineered: Yes
Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Gene: Alpha-Naga
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9k
symmetry Space Group: P 43 21 2
R_factor 0.211 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.593 72.593 176.066 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACY, GOL, NAG, SO4 enzyme Hydrolase E.C.3.2.1.49 BRENDA
related structures by homologous chain: 1KTC
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases., Garman SC, Hannick L, Zhu A, Garboczi DN, Structure (Camb) 2002 Mar;10(3):425-34. PMID:12005440
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (1ktb.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 1KTB
  • CSU: Contacts of Structural Units for 1KTB
  • Likely Quarternary Molecular Structure file(s) for 1KTB
  • Structure Factors (429 Kb)
  • Retrieve 1KTB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KTB from S2C, [Save to disk]
  • Re-refined 1ktb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KTB 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 1KTB
  • 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 1KTB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ktba2, region A:1-293 [Jmol] [rasmolscript] [script source]
        - Domain d1ktba1, region A:294-388 [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: [1ktb_A] [1ktb]
  • SWISS-PROT database: [Q90744]
  • Domain organization of [NAGAB_CHICK] by SWISSPFAM
  • Other resources with information on 1KTB
  • Community annotation for 1KTB 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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