6EA4

ERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor

PDB DOI: https://doi.org/10.2210/pdb6EA4/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2018-08-02 Released: 2019-12-18
Deposition Author(s): Maben, Z., Stern, L.J.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.236
R-Value Work: 0.208
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Crystal structure of human ER aminopeptidase 1 bound to aryl sulfonamide inhibitor.

Maben, Z., Stern, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 218.81 kDa
Atom Count: 15,097
Modelled Residue Count: 1,752
Deposited Residue Count: 1,822
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	911	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: 8	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	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, D, G	5		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain G Interactions & Density Focus chain C Focus chain D Focus chain G
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	E, F, I	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain I Interactions & Density Focus chain E Focus chain F Focus chain I
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	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J2G (Subject of Investigation/LOI) Query on J2G Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B]	L [auth A], X [auth B]	4-methoxy-3-{[2-(piperidin-1-yl)-4-(trifluoromethyl)phenyl]sulfamoyl}benzoic acid C₂₀ H₂₁ F₃ N₂ O₅ S BGLAMEXMBJAJBI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] N [auth A] O [auth A] P [auth A] AA [auth B], BA [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 BA [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 BA [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]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B]	K [auth A], W [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain W [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B]	EA [auth B], M [auth A], R [auth A], Y [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain EA [auth B] Focus chain M [auth A] Focus chain R [auth A] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth B] Focus chain M [auth A] Focus chain R [auth A] Focus chain Y [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain S [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain S [auth A]	CA [auth B], S [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain CA [auth B] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain S [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B]	J [auth A], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain V [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain U [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain U [auth A]	DA [auth B], U [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain U [auth A] Interactions & Density Focus chain DA [auth B] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.236
R-Value Work: 0.208
R-Value Observed: 0.209
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.233	α = 90
b = 135.453	β = 90.11
c = 127.283	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Maben, Z.

Stern, L.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI153828

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2022-06-15
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 3.1: 2023-10-11
Changes: Data collection, Refinement description
Version 3.2: 2024-11-06
Changes: Structure summary

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Help and Resources

6EA4

ERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor

Crystal structure of human ER aminopeptidase 1 bound to aryl sulfonamide inhibitor.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)