7NSK
Endoplasmic reticulum aminopeptidase 2 complexed with a hydroxamic ligand
- PDB DOI: https://doi.org/10.2210/pdb7NSK/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
- Mutation(s): Yes 
- Deposited: 2021-03-08 Released: 2022-06-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.10 Å
- R-Value Free: 0.254 
- R-Value Work: 0.187 
- R-Value Observed: 0.191 
This is version 1.1 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 | 963 | 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 |
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 | C, H | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, I, J, K, L | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | E, F, G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
UQE (Subject of Investigation/LOI) Query on UQE | BA [auth B], S [auth A] | (2~{S})-3-(4-hydroxyphenyl)-~{N}-oxidanyl-2-[4-[[(5-pyridin-2-ylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]propanamide C21 H20 N6 O5 S2 QHHWCHMBFWYFFS-SFHVURJKSA-N | |||
NAG Query on NAG | AA [auth B] N [auth A] O [auth A] P [auth A] Q [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
P4G Query on P4G | R [auth A] | 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N | |||
ZN Query on ZN | M [auth A], Y [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
EDO Query on EDO | T [auth A], U [auth A], V [auth A], W [auth A], X [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.10 Å
- R-Value Free: 0.254 
- R-Value Work: 0.187 
- R-Value Observed: 0.191 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 75.559 | α = 90 |
b = 134.572 | β = 90.2 |
c = 128.638 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2022-06-22  Deposition Author(s): Mpakali, A., Giastas, P., Stratikos, E.
Revision History (Full details and data files)
- Version 1.0: 2022-06-22
Type: Initial release - Version 1.1: 2024-01-31
Changes: Data collection, Refinement description