1Y88 Structural Genomics, Unknown Function date Dec 10, 2004
title Crystal Structure Of Protein Of Unknown Function Af1548
authors V.V.Lunin, E.Evdokimova, M.Kudritskaya, M.E.Cuff, A.Joachimiak, A A.Savchenko, Midwest Center For Structural Genomics (Mcsg)
compound source
Molecule: Hypothetical Protein Af1548
Chain: A
Engineered: Yes
Organism_scientific: Archaeoglobus Fulgidus
Organism_taxid: 2234
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector: Plasmid
Expression_system_plasmid: Modified Pet15b
symmetry Space Group: P 63 2 2
R_factor 0.202 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.225 124.225 62.982 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.85 Å
ligand CL, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1y88.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (1y88.pdb2.gz) 202 Kb
  • Biological Unit Coordinates (1y88.pdb3.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 1Y88
  • CSU: Contacts of Structural Units for 1Y88
  • Likely Quarternary Molecular Structure file(s) for 1Y88
  • Structure Factors (177 Kb)
  • Retrieve 1Y88 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y88 from S2C, [Save to disk]
  • Re-refined 1y88 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y88 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 1Y88
  • 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 1Y88, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y88a1, region A:128-186 [Jmol] [rasmolscript] [script source]
        - Domain d1y88a2, region A:3-127 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y88_A] [1y88]
  • SWISS-PROT database: [O28724]
  • Domain organization of [Y1548_ARCFU] by SWISSPFAM
  • Other resources with information on 1Y88
  • Community annotation for 1Y88 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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