1W8O Hydrolase date Sep 24, 2004
title Contribution Of The Active Site Aspartic Acid To Catalysis I Bacterial Neuraminidase From Micromonospora Viridifaciens
authors S.Newstead, J.N.Watson, V.Dookhun, A.J.Bennet, G.Taylor
compound source
Molecule: Bacterial Sialidase
Chain: A
Fragment: Residues 47-647
Ec: 3.2.1.18
Engineered: Yes
Mutation: Yes
Organism_scientific: Micromonospora Viridifaciens
Organism_taxid: 1881
Atcc: 31146
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 21
R_factor 0.162 R_Free 0.197
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.712 111.168 142.195 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CIT, GAL, GLC, GOL, NA enzyme Hydrolase E.C.3.2.1.18 BRENDA
related structures by homologous chain: 2BER
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceContribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from Micromonospora viridifaciens., Watson JN, Newstead S, Dookhun V, Taylor G, Bennet AJ, FEBS Lett. 2004 Nov 5;577(1-2):265-9. PMID:15527797
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (1w8o.pdb1.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 1W8O
  • CSU: Contacts of Structural Units for 1W8O
  • Likely Quarternary Molecular Structure file(s) for 1W8O
  • Structure Factors (1168 Kb)
  • Retrieve 1W8O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W8O from S2C, [Save to disk]
  • Re-refined 1w8o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1W8O 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 1W8O
  • 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 1W8O, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w8oa1, region A:403-505 [Jmol] [rasmolscript] [script source]
        - Domain d1w8oa3, region A:47-402 [Jmol] [rasmolscript] [script source]
        - Domain d1w8oa2, region A:506-647 [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: [1w8o] [1w8o_A]
  • SWISS-PROT database: [Q02834]
  • Domain organization of [NANH_MICVI] by SWISSPFAM
  • Domain found in 1W8O: [FA58C ] by SMART
  • Other resources with information on 1W8O
  • Community annotation for 1W8O 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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