9S44 | pdb_00009s44

Human Histone Deacetylase SIRT2

PDB DOI: https://doi.org/10.2210/pdb9S44/pdb

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

Deposited: 2025-07-25 Released: 2025-08-20
Deposition Author(s): Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.274 (Depositor), 0.281 (DCC)
R-Value Work:
0.228 (Depositor), 0.234 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Enhancing the potency of sirtuin 2 inhibitors through rational functional group modulations targeting NAD+ co-factor interactions

Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.

To be published.

Macromolecule Content

Total Structure Weight: 34.24 kDa
Atom Count: 2,251
Modeled Residue Count: 279
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	302	Homo sapiens	Mutation(s): 0 Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IXJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.274 (Depositor), 0.281 (DCC)
R-Value Work: 0.228 (Depositor), 0.234 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.76	α = 90
b = 73.51	β = 95.26
c = 54.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	503267011
German Research Foundation (DFG)	Germany	325871075 (SFB1309)

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release

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.