5XHS | pdb_00005xhs

Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA

• PDB DOI: https://doi.org/10.2210/pdb5XHS/pdb

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


• Deposited: 2017-04-24 Released: 2018-05-02 
• Deposition Author(s): Yu, Y., Li, B., Chen, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design

Wang, H.L., Liu, S., Yu, Z.J., Wu, C., Cheng, L., Wang, Y., Chen, K., Zhou, S., Chen, Q., Yu, Y., Li, G.B.

(2017) RSC Adv 7: 36214-36222

• DOI: https://doi.org/10.1039/C7RA05824A

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.11 kDa 
• Atom Count: 2,182 
• Modeled Residue Count: 262 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	288	Homo sapiens	Mutation(s): 0  Gene Names: SIRT5, SIR2L5 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLL	C [auth A]	(2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid C10 H18 N2 O5 ZAFOVBXOMIXMTH-ZETCQYMHSA-N
MCM	D [auth A]	7-AMINO-4-METHYL-CHROMEN-2-ONE C10 H9 N O2 GLNDAGDHSLMOKX-UHFFFAOYSA-N
PHQ	B [auth A]	benzyl chlorocarbonate C8 H7 Cl O2 HSDAJNMJOMSNEV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.13	α = 90
b = 55.274	β = 90
c = 124.303	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Yu, Y., Li, B., Chen, Q.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations