6EA4 | pdb_00006ea4

ERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6EA4

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 
  • Modeled Residue Count: 1,752 
  • Deposited Residue Count: 1,822 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 2
A, B
911Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P179
Glycosylation
Glycosylation Sites: 6
Go to GlyGen: Q6P179-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J2G
(Subject of Investigation/LOI)

Query on J2G


Download:Ideal Coordinates CCD File
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
NAG

Query on NAG


Download:Ideal Coordinates CCD File
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
MES

Query on MES


Download:Ideal Coordinates CCD File
K [auth A],
W [auth B]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
T [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
LYS
(Subject of Investigation/LOI)

Query on LYS


Download:Ideal Coordinates CCD File
EA [auth B],
M [auth A],
R [auth A],
Y [auth B]		LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
IMD

Query on IMD


Download:Ideal Coordinates CCD File
CA [auth B],
S [auth A]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
(Subject of Investigation/LOI)

Query on ZN


Download:Ideal Coordinates CCD File
J [auth A],
V [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
DA [auth B],
U [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J2G BindingDB:  6EA4 IC50: 2.68e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.233α = 90
b = 135.453β = 90.11
c = 127.283γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI153828

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