Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 108.76 kDa 
• Atom Count: 8229 
• Residue Count: 855 
• Unique protein chains: 1

6Q4R

High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor

• DOI: 10.2210/pdb6Q4R/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-12-06 Released: 2019-04-10 
• Deposition Author(s): Giastas, P., Neu, M., Rowland, P., Stratikos, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor.

Giastas, P., Neu, M., Rowland, P., Stratikos, E.

(2019) ACS Med Chem Lett 10: 708-713

• PubMed: 31097987 
• DOI: 10.1021/acsmedchemlett.9b00002
• Primary Citation of Related Structures:  
  6Q4R


• PubMed Abstract: 
  

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that helps generate peptides presented by Major Histocompatibility Complex Class I (MHC class I) molecules and is an emerging target for immunotherapy applications. Despite almost two decades of research on ERAP1, lack of high-resolution crystal structures has hampered drug-development efforts. By optimizing the protein construct, we obtained a high-resolution (1.60 Å) crystal structure of the closed-conformation of ERAP1 with a potent phosphinic pseudopeptide inhibitor bound in its active site. The structure provides key insight on the mechanism of inhibition as well as selectivity toward homologous enzymes and allows detailed mapping of the internal cavity of the enzyme that accommodates peptide-substrates. Bis-tris propane and malic acid molecules, found bound in pockets in the internal cavity, reveal potential druggable secondary binding sites. The ability to obtain high-resolution crystal structures of ERAP1 removes a major bottleneck in the development of compounds that regulate its activity and will greatly accelerate drug-discovery efforts.

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Organizational Affiliation: 

National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum aminopeptidase 1,Endoplasmic reticulum aminopeptidase 1	A	912	Homo sapiens	Mutation(s): 0  Gene Names: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 EC: 3.4.11
Find proteins for Q9NZ08 (Homo sapiens) Explore Q9NZ08  Go to UniProtKB:  Q9NZ08
NIH Common Fund Data Resources
PHAROS:  Q9NZ08 GTEx:  ENSG00000164307

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HJ5	A	[(1~{R})-1-[[(2~{S})-2-[[(2~{S})-1-azaniumyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]pent-4-ynyl]-oxidanyl-phosphoryl]-3-phenyl-propyl]azanium C24 H32 N3 O4 P QCPJTEUURKCRNT-BHIFYINESA-P
B3P	A	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
P6G	A	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	A	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MLT	A	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.683	α = 90
b = 116.669	β = 90
c = 147.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-12-06 
• Released Date: 2019-04-10 
Deposition Author(s): Giastas, P., Neu, M., Rowland, P., Stratikos, E.

Revision History 

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary