2DF5	Hydrolase	date	Feb 24, 2006
title	Crystal Structure Of Pf-Pcp(1-204)-C
authors	Y.Katagiri, K.Takano, H.Chon, H.Matsumura, Y.Koga, S.Kanaya
compound		source
Molecule: Pyrrolidone-Carboxylate Peptidase Chain: A, B, C, D Synonym: Pyrrolidone Carboxyl Peptidase, 5-Oxoprolyl- Pepti Pyroglutamyl-Peptidase I, Pgp-I, Pyrase; Ec: 3.4.19.3 Engineered: Yes Mutation: Yes		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Jm109 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ppcp3-C01
symmetry	Space Group: P 1 21 1	R_factor 0.197 R_Free 0.234
crystal cell	length a length b length c angle alpha angle beta angle gamma 104.240 104.450 48.250 90.00 100.39 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand		enzyme	Hydrolase E.C.3.4.19.3 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Conformational contagion in a protein: Structural properties of a chameleon sequence., Takano K, Katagiri Y, Mukaiyama A, Chon H, Matsumura H, Koga Y, Kanaya S, Proteins. 2007 May 17;68(3):617-625. PMID:17510955

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk] Biological Unit Coordinates (2df5.pdb1.gz) 139 Kb CSU: Contacts of Structural Units for 2DF5 Likely Quarternary Molecular Structure file(s) for 2DF5 Structure Factors (348 Kb) Retrieve 2DF5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DF5 from S2C, [Save to disk] Re-refined 2df5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DF5 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 2DF5

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 2DF5, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2df5] [2df5_D] [2df5_B] [2df5_A] [2df5_C] SWISS-PROT database: [O73944] Domain organization of [PCP_PYRFU] by SWISSPFAM

Other resources with information on 2DF5

Community annotation for 2DF5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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