2YD0 Hydrolase date Mar 17, 2011
title Crystal Structure Of The Soluble Domain Of Human Endoplasmic Aminopeptidase 1 Erap1
authors M.Vollmar, G.Kochan, T.Krojer, E.Ugochukwu, J.R.C.Muniz, J.Raynor A.Chaikuad, C.Allerston, F.Von Delft, C.Bountra, C.H.Arrowsmith J.Weigelt, A.Edwards, S.Knapp
compound source
Molecule: Endoplasmic Reticulum Aminopeptidase 1
Chain: A
Fragment: Soluble Domain, Residues 46-940
Synonym: Adipocyte-Derived Leucine Aminopeptidase, Arts-1, Aminopeptidase Pils, Puromycin-Insensitive Leucyl-Specific Aminopeptidase, Type 1 Tumor Necrosis Factor Receptor Shedd Aminopeptidase Regulator, A-Lap, Pils-Ap;
Ec: 3.4.11.-
Engineered: Yes
Other_details: Glycosylation At Residues Asn70, Asn154, Asn
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: High Five
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfb-Ct10hf-Lic
symmetry Space Group: P 6 2 2
R_factor 0.152 R_Free 0.215
length a length b length c angle alpha angle beta angle gamma
200.948 200.948 114.222 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand BES, EDO, K, NAG, ZN enzyme Hydrolase E.C.3.4.11 BRENDA
note 2YD0 supersedes 2XDT
subcellular loc. Membrane localization by OPM: Endoplasmic reticulum membrane
luminal side
cytoplasmic side

Primary referenceCrystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming., Kochan G, Krojer T, Harvey D, Fischer R, Chen L, Vollmar M, von Delft F, Kavanagh KL, Brown MA, Bowness P, Wordsworth P, Kessler BM, Oppermann U, Proc Natl Acad Sci U S A. 2011 May 10;108(19):7745-50. Epub 2011 Apr 20. PMID:21508329
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (2yd0.pdb1.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 2YD0
  • CSU: Contacts of Structural Units for 2YD0
  • Structure Factors (542 Kb)
  • Retrieve 2YD0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YD0 from S2C, [Save to disk]
  • Re-refined 2yd0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YD0 in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2YD0
  • 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 2YD0, from MSDmotif at EBI
  • Fold representative 2yd0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yd0] [2yd0_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YD0
  • Community annotation for 2YD0 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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