2YD0

Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1

Structural Biology Knowledgebase: 2YD0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.152

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YD0

Classification: HYDROLASE

Total Structure Weight: 104181.04

Macromolecule Entities
Molecule Chains Length Organism Details
ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 A 897 Homo sapiens EC#: 3.4.11 IUBMB
Fragment: SOLUBLE DOMAIN, RESIDUES 46-940
Details: GLYCOSYLATION AT RESIDUES ASN70, ASN154, ASN414
Gene Name(s): ERAP1 Gene View APPILS ARTS1 KIAA0525 UNQ584/PRO1154

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

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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.152
  • Space Group: P 6 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 200.95 α = 90.00
b = 200.95 β = 90.00
c = 114.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-17
  • Released Date: 2011-04-13
  • Deposition author(s): Vollmar, M., Kochan, G., Krojer, T., Ugochukwu, E., Muniz, J.R.C., Raynor, J., Chaikuad, A., Allerston, C., Von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S.
  • Previous versions: 2XDT

Revision History

  • 2012-10-03
    Type: Source and taxonomy | Details: SOURCE
  • 2012-10-03
    Type: Version format compliance | Details: REMARK 4
  • 2012-10-03
    Type: Citation | Details: JRNL