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 Diffraction	resolution	2.60 Å
ligand	ACY, SO4, ZN	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal 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] (110 Kb) [Save to disk] Biological Unit Coordinates (3af5.pdb1.gz) 105 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

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 3AF5, from MSDmotif at EBI

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)

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