6L72 | pdb_00006l72

Sirtuin 2 demyristoylation native final product

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli K-12
  • Mutation(s): No 

  • Deposited: 2019-10-30 Released: 2021-03-31 
  • Deposition Author(s): Chen, L.F.
  • Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.243 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6L72

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.

Macromolecule Content 

  • Total Structure Weight: 35.24 kDa 
  • Atom Count: 2,472 
  • Modeled Residue Count: 294 
  • Deposited Residue Count: 304 
  • Unique protein chains: 1

Macromolecules

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|  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 (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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OMR
(Subject of Investigation/LOI)

Query on OMR


Download:Ideal Coordinates CCD File
B [auth A][(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate
C29 H49 N5 O15 P2
UIDOGMGTRGOBRS-FMKANDLMSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.243 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.736α = 90
b = 77.572β = 97.35
c = 56.072γ = 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: Data collection, Database references, Refinement description