6L65 | pdb_00006l65

Sirtuin 2 protein with H3K18 myristoylated peptide

• PDB DOI: https://doi.org/10.2210/pdb6L65/pdb

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


• Deposited: 2019-10-28 Released: 2020-11-04 
• 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: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.179 (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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.63 kDa 
• Atom Count: 2,768 
• Modeled Residue Count: 292 
• Deposited Residue Count: 312 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	307	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	B [auth C]	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYR (Subject of Investigation/LOI)	D [auth C]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.062	α = 90
b = 73.399	β = 93.86
c = 55.693	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Chen, L.F.

---

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

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary