7NUP

Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand

PDB DOI: https://doi.org/10.2210/pdb7NUP/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): Yes

Deposited: 2021-03-12 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: 0.267
R-Value Work: 0.182
R-Value Observed: 0.186

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 complexed with a mixed hydroxamic and sulfonyl ligand

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

To be published.

Macromolecule Content

Total Structure Weight: 461.3 kDa
Atom Count: 29,963
Modelled Residue Count: 3,589
Deposited Residue Count: 3,864
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum aminopeptidase 2	A, B, C, D	966	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
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q6P179-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, Q	4		N-Glycosylation	Interactions Focus chain E Focus chain Q Interactions & Density Focus chain E Focus chain Q
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	F, G, J, K, L F, G, J, K, L, M, P, S	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain S Interactions & Density Focus chain F Focus chain G Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain S
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	H, I, O, R	3		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain O Focus chain R Interactions & Density Focus chain H Focus chain I Focus chain O Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
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	N	5		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
USK Query on USK Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain GB [auth D] SDF format, chain PA [auth B] SDF format, chain YA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain PA [auth B] MOL2 format, chain YA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain PA [auth B] mmCIF format, chain YA [auth C]	AA [auth A], GB [auth D], PA [auth B], YA [auth C]	(3~{S})-4-(4-hydroxyphenyl)-~{N}-oxidanyl-3-[5-[[(5-phenylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]butanamide C₂₃ H₂₃ N₅ O₅ S₂ YNJVRCJGXCXRMB-SFHVURJKSA-N		Interactions Focus chain AA [auth A] Focus chain GB [auth D] Focus chain PA [auth B] Focus chain YA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain GB [auth D] Focus chain PA [auth B] Focus chain YA [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	CB [auth D] DB [auth D] EB [auth D] FB [auth D] MA [auth B] CB [auth D], DB [auth D], EB [auth D], FB [auth D], MA [auth B], NA [auth B], OA [auth B], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain Z [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain BA [auth A]	BA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth D] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain ZA [auth C]	AB [auth C] DA [auth A] EA [auth A] FA [auth A] GA [auth A] AB [auth C], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], IB [auth D], JA [auth A], KA [auth A], RA [auth B], SA [auth B], ZA [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AB [auth C] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain ZA [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain LA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth C] MOL2 format, chain BB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] mmCIF format, chain BB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C]	BB [auth D], LA [auth B], T [auth A], TA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain LA [auth B] Focus chain T [auth A] Focus chain TA [auth C] Interactions & Density Focus chain BB [auth D] Focus chain LA [auth B] Focus chain T [auth A] Focus chain TA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain HB [auth D] SDF format, chain QA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain QA [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain QA [auth B]	CA [auth A], HB [auth D], QA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain HB [auth D] Focus chain QA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain HB [auth D] Focus chain QA [auth B]