7NSK

Endoplasmic reticulum aminopeptidase 2 complexed with a hydroxamic ligand


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 2A, B963Homo sapiensMutation(s): 1 
Gene Names: ERAP2LRAP
EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P179 (Homo sapiens)
Explore Q6P179 
Go to UniProtKB:  Q6P179
PHAROS:  Q6P179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P179
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseC, H 5N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, I, J, K, L 2N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G 3N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQE (Subject of Investigation/LOI)
Query on UQE

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
P4G
Query on P4G

Download Ideal Coordinates CCD File 
R [auth A]1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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 = 75.559α = 90
b = 134.572β = 90.2
c = 128.638γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release