3MDJ Hydrolase Hydrolase Inhibitor date Mar 30, 2010
title Er Aminopeptidase, Erap1, Bound To The Zinc Aminopeptidase I Bestatin
authors T.T.Nguyen, L.J.Stern
compound source
Molecule: Endoplasmic Reticulum Aminopeptidase 1
Chain: A, B, C
Fragment: Unp Residues 37-939
Synonym: Adipocyte-Derived Leucine Aminopeptidase, A-Lap, A Aminopeptidase Pils, Puromycin-Insensitive Leucyl-Specific Aminopeptidase, Pils-Ap, Type 1 Tumor Necrosis Factor Recep Shedding Aminopeptidase Regulator;
Ec: 3.4.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erap1, Appils, Arts1, Kiaa0525, Unq584pro1154
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Hi5
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
71.029 234.635 95.860 90.00 103.59 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand BES, BMA, MAN, NAG, ZN enzyme Hydrolase E.C.3.4.11 BRENDA
subcellular loc. Membrane localization by OPM: Endoplasmic reticulum membrane
luminal side
cytoplasmic side
A, C, B

Primary referenceStructural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1., Nguyen TT, Chang SC, Evnouchidou I, York IA, Zikos C, Rock KL, Goldberg AL, Stratikos E, Stern LJ, Nat Struct Mol Biol. 2011 May;18(5):604-13. Epub 2011 Apr 10. PMID:21478864
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (858 Kb) [Save to disk]
  • Biological Unit Coordinates (3mdj.pdb1.gz) 287 Kb
  • Biological Unit Coordinates (3mdj.pdb2.gz) 288 Kb
  • Biological Unit Coordinates (3mdj.pdb3.gz) 288 Kb
  • LPC: Ligand-Protein Contacts for 3MDJ
  • CSU: Contacts of Structural Units for 3MDJ
  • Structure Factors (941 Kb)
  • Retrieve 3MDJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MDJ from S2C, [Save to disk]
  • Re-refined 3mdj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MDJ 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 3MDJ
  • 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 3MDJ, from MSDmotif at EBI
  • Fold representative 3mdj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mdj_C] [3mdj_A] [3mdj] [3mdj_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MDJ
  • Community annotation for 3MDJ 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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