7NSK | pdb_00007nsk

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
Deposition Author(s): Mpakali, A., Giastas, P., Stratikos, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.187 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Endoplasmic reticulum aminopeptidase 2 in complex with a phosphinic ligand

Mpakali, A., Giastas, P., Stratikos, E.

To be published.

Macromolecule Content

Total Structure Weight: 230.66 kDa
Atom Count: 15,016
Modeled Residue Count: 1,789
Deposited Residue Count: 1,926
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum aminopeptidase 2	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P179
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q6P179-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Focus chain H Interactions & Density Focus chain C Focus chain H
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain D Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain D Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain E Focus chain F Focus chain G
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 Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain BA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain BA [auth B]	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		Interactions Focus chain BA [auth B] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain S [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain AA [auth B]	AA [auth B] N [auth A] O [auth A] P [auth A] Q [auth A] AA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Z [auth B]
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain M [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain M [auth A]	M [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain Y [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A]	T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]