1KER Lyase date Nov 17, 2001
title The Crystal Structure Of Dtdp-D-Glucose 4,6-Dehydratase (Rml Streptococcus Suis With Dtdp-D-Glucose Bound
authors S.T.M.Allard, K.Beis, M.F.Giraud, A.D.Hegeman, J.W.Gross, C.Whit M.Graninger, P.Messner, A.G.Allen, J.H.Naismith
compound source
Molecule: Dtdp-D-Glucose 4,6-Dehydratase
Chain: A, B
Synonym: Rmlb
Ec: 4.2.1.46
Engineered: Yes
Organism_scientific: Streptococcus Suis
Organism_taxid: 1307
Variant: Serotype 2
Gene: Rmlb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.225 96.151 182.888 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand DAU, NAD, SO4 enzyme Lyase E.C.4.2.1.46 BRENDA
related structures by homologous chain: 1KET
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceToward a structural understanding of the dehydratase mechanism., Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH, Structure (Camb) 2002 Jan;10(1):81-92. PMID:11796113
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (1ker.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 1KER
  • CSU: Contacts of Structural Units for 1KER
  • Likely Quarternary Molecular Structure file(s) for 1KER
  • Retrieve 1KER in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KER from S2C, [Save to disk]
  • View 1KER 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 1KER
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1KER, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kera_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kerb_, region B [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: [1ker_B] [1ker_A] [1ker]
  • SWISS-PROT database: [P95780]
  • Domain organization of [RMLB_STRMU] by SWISSPFAM
  • Other resources with information on 1KER
  • Community annotation for 1KER 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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