6ACP

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H4K91

• PDB DOI: https://doi.org/10.2210/pdb6ACP/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H4K91

Hang, T.R., Chen, W.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.06 kDa 
• Atom Count: 2,108 
• Modelled Residue Count: 272 
• Deposited Residue Count: 274 
• 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 H4K91	B	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

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
SLL	B	L-PEPTIDE LINKING	C10 H18 N2 O5		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.078	α = 90
b = 41.267	β = 108.37
c = 61.334	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.

---

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