24OJ | pdb_000024oj

SIRT2 structure in complex with H3K18myr peptide collected by Laue diffraction

• PDB DOI: https://doi.org/10.2210/pdb24OJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-03-13 Released: 2026-11-11 
• Deposition Author(s): Zhang, N., Hao, Q.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.239 (DCC) 

Starting Model: experimental

Literature

SIRT2 structure in complex with H3K18myr peptide collected by Laue diffraction

Zhang, N., Hao, Q.

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: 35.7 kDa 
• Atom Count: 2,260 
• Modeled Residue Count: 283 
• Deposited Residue Count: 313 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	B [auth C]	307	Homo sapiens	Mutation(s): 0  Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6  Go to UniProtKB:  Q8IXJ6
GTEx:  ENSG00000068903

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.239 (DCC) 

Diffraction Data: https://doi.org/10.12402/photon/laue/dataset-20260128111033

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.9	α = 90
b = 74.5	β = 92.4
c = 56.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Laueprocess	data reduction
LSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Zhang, N., Hao, Q.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	0000-0001-9961-9046

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release