6L71 | pdb_00006l71

Sirtuin 2 demyristoylation native intermediate I & II mixture

• PDB DOI: https://doi.org/10.2210/pdb6L71/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.224 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Sirtuin 2 protein with H3K18 myristoylated peptide

Chen, L.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.74 kDa 
• Atom Count: 2,761 
• Modeled Residue Count: 302 
• Deposited Residue Count: 310 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	304	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-ARG-LYS-GLN-LEU-ALA	B [auth C]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDD (Subject of Investigation/LOI)	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)	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)	C [auth A]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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), 0.169 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.601	α = 90
b = 78.095	β = 97.64
c = 56.347	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	HKU/C7037-14G

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary