5Z93 | pdb_00005z93

Crystal Structure of SIRT3 in complex with H3K9bhb peptide

• PDB DOI: https://doi.org/10.2210/pdb5Z93/pdb

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


• Deposited: 2018-02-02 Released: 2019-02-06 
• Deposition Author(s): Zhang, X., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal Structure of SIRT3 in complex with H3K9bhb peptide

Zhang, X., Li, H.

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 32.56 kDa 
• Atom Count: 2,427 
• Modeled Residue Count: 281 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	283	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7 GTEx:  ENSG00000142082

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gene for histone H3 (germline gene)	B	10	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for V9H1G0 (Homo sapiens) Explore V9H1G0  Go to UniProtKB:  V9H1G0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KHB	B	L-PEPTIDE LINKING	C10 H20 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.361	α = 90
b = 86.025	β = 90
c = 88.431	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Zhang, X., Li, H.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary