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 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-2304Homo sapiensMutation(s): 0 
Gene Names: SIRT2, SIR2L, SIR2L2
EC: 2.3.1.286
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • 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

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Ligand Structure Quality Assessment 


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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