2OKN Hydrolase date Jan 17, 2007
title Crystal Strcture Of Human Prolidase
authors U.Mueller, F.H.Niesen, Y.Roske, F.Goetz, J.Behlke, K.Buessow, U.He Protein Structure Factory (Psf)
compound source
Molecule: Xaa-Pro Dipeptidase
Chain: A, B
Synonym: X-Pro Dipeptidase, Proline Dipeptidase, Prolidase, Imidodipeptidase;
Ec: 3.4.13.9
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pepd, Prd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Scs1prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Rzpd Clone Id Psfep250h122
symmetry Space Group: C 2 2 21
R_factor 0.178 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.890 108.960 212.010 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand MN, PI enzyme Hydrolase E.C.3.4.13.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (2okn.pdb1.gz) 158 Kb
  • LPC: Ligand-Protein Contacts for 2OKN
  • CSU: Contacts of Structural Units for 2OKN
  • Likely Quarternary Molecular Structure file(s) for 2OKN
  • Structure Factors (665 Kb)
  • Retrieve 2OKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OKN from S2C, [Save to disk]
  • Re-refined 2okn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OKN 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 2OKN
  • 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 2OKN, from MSDmotif at EBI
  • Fold representative 2okn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2okn]
  • SWISS-PROT database: [P12955]
  • Domain organization of [PEPD_HUMAN] by SWISSPFAM
  • Domain found in 2OKN: [AMP_N ] by SMART
  • Alignments of the sequence of 2OKN with the sequences similar proteins can be viewed for 2OKN's classification [PEPD_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PEPD_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2OKN
  • Community annotation for 2OKN 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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