7X3P | pdb_00007x3p

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

• PDB DOI: https://doi.org/10.2210/pdb7X3P/pdb

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


• Deposited: 2022-03-01 Released: 2023-09-06 
• Deposition Author(s): Li, G.-B., Deng, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.163 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

Li, G.-B., Deng, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.03 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 267 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	277	Homo sapiens	Mutation(s): 0  Gene Names: SIRT5, SIR2L5 EC: 2.3.1
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8VG (Subject of Investigation/LOI)	B [auth A]	5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid C31 H33 F3 N6 O6 S BSPJSERNTAGWAV-OZXSUGGESA-N
PEG (Subject of Investigation/LOI)	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.163 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.332	α = 90
b = 65.034	β = 93.58
c = 55.658	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Li, G.-B., Deng, J.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82122065, 82073698

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary