2DQM Hydrolase date May 29, 2006
title Crystal Structure Of Aminopeptidase N Complexed With Bestati
authors Y.Onohara, Y.Nakajima, K.Ito, T.Yoshimoto
compound source
Molecule: Aminopeptidase N
Chain: A
Synonym: Alpha-Aminoacylpeptide Hydrolase
Ec: 3.4.11.2
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Pepn
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1-Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbluescript Sk II(-)
symmetry Space Group: P 31 2 1
R_factor 0.182 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.417 120.417 170.859 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
ligand BES, SO4, ZN enzyme Hydrolase E.C.3.4.11.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure of Aminopeptidase N (Proteobacteria Alanyl Aminopeptidase) from Escherichia coli and Conformational Change of Methionine 260 Involved in Substrate Recognition., Ito K, Nakajima Y, Onohara Y, Takeo M, Nakashima K, Matsubara F, Ito T, Yoshimoto T, J Biol Chem. 2006 Nov 3;281(44):33664-76. Epub 2006 Aug 2. PMID:16885166
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (2dqm.pdb1.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 2DQM
  • CSU: Contacts of Structural Units for 2DQM
  • Likely Quarternary Molecular Structure file(s) for 2DQM
  • Structure Factors (6211 Kb)
  • Retrieve 2DQM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DQM from S2C, [Save to disk]
  • Re-refined 2dqm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DQM 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 2DQM
  • 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 2DQM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dqm_A] [2dqm]
  • SWISS-PROT database: [P04825]
  • Domain organization of [AMPN_ECOLI] by SWISSPFAM
  • Other resources with information on 2DQM
  • Community annotation for 2DQM 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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