8QTU | pdb_00008qtu

Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-3 and NAD+

• PDB DOI: https://doi.org/10.2210/pdb8QTU/pdb

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


• Deposited: 2023-10-13 Released: 2024-10-23 
• Deposition Author(s): Friedrich, F., Kalbas, D., Meleshin, M., Einsle, O., Schutkowski, M., Jung, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

New Super-Slow Substrates as novel Sirtuin-Inhibitors

Friedrich, F., Kalbas, D., Einsle, O., Jung, M., Schutkowski, M.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 36.52 kDa 
• Atom Count: 2,664 
• Modelled Residue Count: 291 
• Deposited Residue Count: 313 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	304	Homo sapiens	Mutation(s): 0  Gene Names: SIRT2, SIR2L, SIR2L2 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 Q8IXJ6 (Homo sapiens) Explore Q8IXJ6  Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6 GTEx:  ENSG00000068903

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide-based super-slow substrate TNFn-3	B	9	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
WWE (Subject of Investigation/LOI)	F [auth B]	3-dodecylsulfanyl-3-methyl-butanoic acid C17 H34 O2 S FVOHTIJLQOWWCZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NIY	B	L-PEPTIDE LINKING	C9 H10 N2 O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.292	α = 90
b = 74.689	β = 97.66
c = 56.197	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Friedrich, F., Kalbas, D., Meleshin, M., Einsle, O., Schutkowski, M., Jung, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 992
German Research Foundation (DFG)	Germany	295/18-1

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release