3MDJ

ER Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin

Structural Biology Knowledgebase: 3MDJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3MDJ

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 319749.53

Macromolecule Entities
Molecule Chains Length Organism Details
Endoplasmic reticulum aminopeptidase 1 A, B, C 921 Homo sapiens EC#: 3.4.11 IUBMB
Fragment: UNP residues 37-939
Mutation: G346D, G514R, K528R, Q730E
Gene Name(s): ERAP1 Gene View APPILS ARTS1 KIAA0525 UNQ584/PRO1154
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BES
Query on BES

A, B, C 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)- 4-METHYL-PENTANOIC ACID
BESTATIN (Synonym)
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, C ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.199
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.03 α = 90.00
b = 234.63 β = 103.59
c = 95.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-30
  • Released Date: 2011-03-30
  • Deposition author(s): Nguyen, T.T., Stern, L.J.

Revision History

  • 2011-07-27
    Type: Other | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4