3AF5 Hydrolase date Feb 23, 2010
title The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404 Fr Pyrococcus Horikoshii
authors Y.Nishida, H.Ishikawa, N.Nakagawa, R.Masui, S.Kuramitsu
compound source
Molecule: Putative Uncharacterized Protein Ph1404
Chain: A
Engineered: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 70601
Strain: Ot3
Gene: Ph1404
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-11a
symmetry Space Group: P 43 21 2
R_factor 0.196 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.200 86.200 238.287 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand ACY, SO4, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii., Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R, Proteins. 2010 Aug 1;78(10):2395-8. PMID:20544974
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (3af5.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 3AF5
  • CSU: Contacts of Structural Units for 3AF5
  • Structure Factors (466 Kb)
  • Retrieve 3AF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AF5 from S2C, [Save to disk]
  • Re-refined 3af5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AF5 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 3AF5
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3AF5, from MSDmotif at EBI
  • Fold representative 3af5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3af5_A] [3af5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AF5: [Beta-Casp] [KH] [Lactamase_B ] by SMART
  • Other resources with information on 3AF5
  • Community annotation for 3AF5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science