2YD0

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

• PDB DOI: https://doi.org/10.2210/pdb2YD0/pdb
• Entry: 2YD0 supersedes: 2XDT

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2011-03-17 Released: 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.18 kDa 
• Atom Count: 7,239 
• Modelled Residue Count: 858 
• Deposited Residue Count: 897 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1	A	897	Homo sapiens	Mutation(s): 0  EC: 3.4.11 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ08 (Homo sapiens) Explore Q9NZ08  Go to UniProtKB:  Q9NZ08
PHAROS:  Q9NZ08 GTEx:  ENSG00000164307

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BES	I [auth A]	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID C16 H24 N2 O4 VGGGPCQERPFHOB-RDBSUJKOSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.948	α = 90
b = 200.948	β = 90
c = 114.222	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• 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.
• This entry supersedes: 2XDT

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references, Source and taxonomy, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2019-03-27
  Changes: Data collection, Derived calculations
• Version 1.4: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary