1FY6 Lyase date Sep 28, 2000
title Aquifex Aeolicus Kdo8p Synthase In Complex With Cadmium And
authors H.S.Duewel, S.Radaev, J.Wang, R.W.Woodard, D.L.Gatti
compound source
Molecule: 2-Dehydro-3-Deoxyphosphooctonate Aldolase
Chain: A, B
Synonym: Kdo8p Synthase, Phospho-2-Dehydro-3-Deoxyoctonate 3-Deoxy-D-Manno-Octulosonic Acid 8-Phosphate Synthetase, Kd Phosphate Synthetase;
Ec: 4.1.2.16
Engineered: Yes
Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Paakdsa
symmetry Space Group: P 31 2 1
R_factor 0.219 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.671 84.671 160.036 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.89 Å
ligand A5P, CD, PO4 enzyme Lyase E.C.4.1.2.16 BRENDA
related structures by homologous chain: 1FWS, 1T99
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSubstrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism., Duewel HS, Radaev S, Wang J, Woodard RW, Gatti DL, J Biol Chem 2001 Mar 16;276(11):8393-402. PMID:11115499
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1fy6.pdb1.gz) 171 Kb
  • LPC: Ligand-Protein Contacts for 1FY6
  • CSU: Contacts of Structural Units for 1FY6
  • Likely Quarternary Molecular Structure file(s) for 1FY6
  • Structure Factors (563 Kb)
  • Retrieve 1FY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FY6 from S2C, [Save to disk]
  • Re-refined 1fy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1FY6 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 1FY6
  • 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 1FY6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fy6a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fy6b_, 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: [1fy6] [1fy6_B] [1fy6_A]
  • SWISS-PROT database: [O66496]
  • Domain organization of [KDSA_AQUAE] by SWISSPFAM
  • Other resources with information on 1FY6
  • Community annotation for 1FY6 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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