SAXSdb — 9fdx

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent protein deacetylase sirtuin-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 DIMETHYL SULFOXIDE × 3 1,2-ETHANEDIOL × 2 ;(2~{S})-2-acetamido-~{N}-[(2~{S},3~{R})-1-azanyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]-6-[[(3~{R})-3-(3,4-dichlorophenyl)sulfanylbutanoyl]amino]hexanamide ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–304； UniProt 56–356

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9fdx
Deposition date deposition_date	2024-05-17
Structure title title	Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9
Keywords keywords	Inhibitor, Sirtuin 2, Deacylase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9fdx__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9fdx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fdx__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.33 Å
Rg (electron density)	20.31 Å
Total Rg	21.25 Å
Atom count	2354
Residues	288
Excluded volume	42186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fdx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NAD-dependent protein deacetylase sirtuin-2
Molecular weight formula_weight	34416.7 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2624

GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;(2~{S})-2-acetamido-~{N}-[(2~{S},3~{R})-1-azanyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]-6-[[(3~{R})-3-(3,4-dichlorophenyl)sulfanylbutanoyl]amino]hexanamide ;
Molecular weight formula_weight	535.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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Unit-cell length a length_a	36.121 Å
Unit-cell length b length_b	73.248 Å
Unit-cell length c length_c	55.178 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	54.950 Å
R factor r_factor	0.1791
R_work r_work	0.1777
R_free r_free	0.2057

Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent protein deacetylase sirtuin-2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fdx__assembly_1__model_1

9fdx__assembly_1__model_1 | I(q)

9fdx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent protein deacetylase sirtuin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9fdx__assembly_1__model_1

9fdx__assembly_1__model_1 | I(q)

9fdx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)