8QT8 | pdb_00008qt8

Crystal structure of human Sirt2 in complex with a TNFa-Myr analogue TNFn-34

PDB DOI: https://doi.org/10.2210/pdb8QT8/pdb

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

Deposited: 2023-10-12 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

New Super-Slow Substrates as novel Sirtuin-Inhibitors

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

To be published.

Macromolecule Content

Total Structure Weight: 35.76 kDa
Atom Count: 2,587
Modeled Residue Count: 296
Deposited Residue Count: 314
Unique protein chains: 2

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IXJ6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide-based TNFa-Myr analogue TNFn-34	B	10	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WWK (Subject of Investigation/LOI) Query on WWK Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3-dodecylsulfanylpropanoic acid C₁₅ H₃₀ O₂ S VKLOPQHLJNFYKK-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.212 (Depositor), 0.212 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.106	α = 90
b = 73.339	β = 95.17
c = 55.229	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Schutkowski, M.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.