5J6S
Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative ligand
- PDB DOI: https://doi.org/10.2210/pdb5J6S/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2016-04-05 Released: 2017-03-15 
- Funding Organization(s): European Union and the Greek Secretariat for Research and Technology (Bilateral Greece-France collaboration action)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.276 
- R-Value Work: 0.205 
- R-Value Observed: 0.208 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Endoplasmic reticulum aminopeptidase 2 | 967 | Homo sapiens | Mutation(s): 1  Gene Names: ERAP2, LRAP EC: 3.4.11 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q6P179 (Homo sapiens) Explore Q6P179  Go to UniProtKB:  Q6P179 | |||||
PHAROS:  Q6P179 GTEx:  ENSG00000164308  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6P179 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | C, E | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
6GA Query on 6GA | O [auth A], V [auth B] | (2S)-N~1~-benzyl-2-[(4-fluorophenyl)methyl]-N~3~-hydroxypropanediamide C17 H17 F N2 O3 UBULRDFJXZRBJH-HNNXBMFYSA-N | |||
NAG Query on NAG | I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | H [auth A], P [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.276 
- R-Value Work: 0.205 
- R-Value Observed: 0.208 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 73.54 | α = 90 |
b = 134.33 | β = 91.71 |
c = 127.58 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-03-15  Deposition Author(s): Saridakis, E., Giastas, P., Mpakali, A., Deprez-Poulain, R., Stratikos, E.
Funding Organization | Location | Grant Number |
---|---|---|
European Union and the Greek Secretariat for Research and Technology (Bilateral Greece-France collaboration action) | Greece | HIAP |
Revision History (Full details and data files)
- Version 1.0: 2017-03-15
Type: Initial release - Version 1.1: 2017-04-05
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary