6ACE | pdb_00006ace

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122

• PDB DOI: https://doi.org/10.2210/pdb6ACE/pdb

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


• Deposited: 2018-07-26 Released: 2019-07-24 
• Deposition Author(s): Hang, T.R., Chen, W.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122

Hang, T.R., Chen, W.B., Zang, J.Y., Zhang, X.

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)

Macromolecule Content 

• Total Structure Weight: 30.35 kDa 
• Atom Count: 2,255 
• Modeled Residue Count: 275 
• Deposited Residue Count: 275 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	267	Homo sapiens	Mutation(s): 0  Gene Names: SIRT5 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens) Explore Q9NXA8  Go to UniProtKB:  Q9NXA8
PHAROS:  Q9NXA8 GTEx:  ENSG00000124523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
succinyl peptide H3K122	B	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLL	B	L-PEPTIDE LINKING	C10 H18 N2 O5		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.227	α = 90
b = 41.169	β = 94.69
c = 55.854	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Hang, T.R., Chen, W.B.

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Funding Organization	Location	Grant Number
	China	2017YFA0503600
	China	2016YFA0400903
	China	XDB19000000
	China	31621002
	China	U1532109
	China	31700671
	China	2017FXCX004
	China	1608085QC52

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description