6L71

Sirtuin 2 demyristoylation native intermediate I & II mixture


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.224 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YDDClick on this verticalbar to view detailsBest fitted YOYClick on this verticalbar to view detailsBest fitted NCAClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Sirtuin 2 protein with H3K18 myristoylated peptide

Chen, L.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-2304Homo sapiensMutation(s): 0 
Gene Names: SIRT2SIR2LSIR2L2
EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens)
Explore Q8IXJ6 
Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6
GTEx:  ENSG00000068903 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXJ6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PRO-ARG-LYS-GLN-LEU-ALAB [auth C]6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YDD (Subject of Investigation/LOI)
Query on YDD

Download Ideal Coordinates CCD File 
E [auth C][[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate
C29 H51 N5 O14 P2
XDVQERDQBQWVRC-UHUMEYFMSA-N
YOY (Subject of Investigation/LOI)
Query on YOY

Download Ideal Coordinates CCD File 
D [auth C][[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C28 H47 N5 O14 P2
KJBRVZZXXRAVKC-XBVYZWAMSA-N
NCA (Subject of Investigation/LOI)
Query on NCA

Download Ideal Coordinates CCD File 
C [auth A]NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NCA BindingDB:  6L71 IC50: min: 1200, max: 1.01e+5 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.224 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.601α = 90
b = 78.095β = 97.64
c = 56.347γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YDDClick on this verticalbar to view detailsBest fitted YOYClick on this verticalbar to view detailsBest fitted NCAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2021-03-31 
  • Deposition Author(s): Chen, L.F.

Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongHKU/C7037-14G

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Advisory, Data collection, Database references, Refinement description