2D5L	Hydrolase	date	Nov 02, 2005
title	Crystal Structure Of Prolyl Tripeptidyl Aminopeptidase From Porphyromonas Gingivalis
authors	Y.Nakajima, K.Ito, Y.Xu, N.Yamada, Y.Onohara, T.Yoshimoto
compound		source
Molecule: Dipeptidyl Aminopeptidase Iv, Putative Chain: A Fragment: Residues 39-732 Synonym: Prolyl Tripeptidyl Aminopeptidase Ec: 3.4.14.- Engineered: Yes		Organism_scientific: Porphyromonas Gingivalis Organism_taxid: 242619 Strain: W83 Gene: Pg1361 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: M15 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pqe-30
symmetry	Space Group: P 63 2 2	R_factor 0.203 R_Free 0.228
crystal cell	length a length b length c angle alpha angle beta angle gamma 149.394 149.394 159.684 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	SO4	enzyme	Hydrolase E.C.3.4.14 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis., Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T, J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:16914159

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk] Biological Unit Coordinates (2d5l.pdb1.gz) 223 Kb LPC: Ligand-Protein Contacts for 2D5L CSU: Contacts of Structural Units for 2D5L Likely Quarternary Molecular Structure file(s) for 2D5L Structure Factors (1492 Kb) Retrieve 2D5L in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D5L from S2C, [Save to disk] Re-refined 2d5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D5L 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 2D5L

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 2D5L, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d5l] [2d5l_A] SWISS-PROT database: [Q7MUW6] Domain organization of [Q7MUW6_PORGI] by SWISSPFAM

Other resources with information on 2D5L

Community annotation for 2D5L at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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