1YH8 Hydrolase date Jan 07, 2005
title Crystal Structure Of Aquifex Aeolicus Lpxc Deacetylase Complexed With Palmitate
authors M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke
compound source
Molecule: Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase;
Chain: A, B
Synonym: Udp-3-O-Acyl-Glcnac Deacetylase
Ec: 3.5.1.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363
Gene: Lpxc, Enva
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 61
R_factor 0.201 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.610 101.610 124.180 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand CL, PAM, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
related structures by homologous chain: 1XXE, 1YHC
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceUDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine Deacetylase Functions through a General Acid-Base Catalyst Pair Mechanism., Hernick M, Gennadios HA, Whittington DA, Rusche KM, Christianson DW, Fierke CA, J Biol Chem 2005 Apr 29;280(17):16969-78. Epub 2005 Feb 10. PMID:15705580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (1yh8.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 1YH8
  • CSU: Contacts of Structural Units for 1YH8
  • Likely Quarternary Molecular Structure file(s) for 1YH8
  • Retrieve 1YH8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YH8 from S2C, [Save to disk]
  • View 1YH8 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 1YH8
  • 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 1YH8, from MSDmotif at EBI
  • Fold representative 1yh8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yh8] [1yh8_A] [1yh8_B]
  • SWISS-PROT database: [O67648]
  • Domain organization of [LPXC_AQUAE] by SWISSPFAM
  • Other resources with information on 1YH8
  • Community annotation for 1YH8 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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