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
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

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.

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