SAXSdb — 1q17

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

HST2 protein

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 3 CHLORIDE ION × 4 ADENOSINE-5-DIPHOSPHORIBOSE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HST2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–300； UniProt 1–294 Author chain B； PDBConstruct 7–300； UniProt 1–294 Author chain C； PDBConstruct 7–300； UniProt 1–294

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	1q17
Deposition date deposition_date	2003-07-18
Structure title title	Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide
Keywords keywords	histone deacetylase, 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.

1q17__assembly_1__model_1

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

Download this curve (.dat)

1q17__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1q17__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.30 Å
Rg (electron density)	31.64 Å
Total Rg	32.35 Å
Atom count	7099
Residues	879
Excluded volume	126960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1q17__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	HST2 protein
Molecular weight formula_weight	33809.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7261

HHGMASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
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	3

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5-DIPHOSPHORIBOSE
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1q17a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1q17a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1q17b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1q17b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1q17c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1q17c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1q17A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1q17A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1q17B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1q17B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1q17C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1q17C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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Unit-cell length a length_a	146.159 Å
Unit-cell length b length_b	109.682 Å
Unit-cell length c length_c	85.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	28.880 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2470

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide

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

HST2 protein

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

1q17__assembly_1__model_1

1q17__assembly_1__model_1 | I(q)

1q17__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide

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

HST2 protein

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

1q17__assembly_1__model_1

1q17__assembly_1__model_1 | I(q)

1q17__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)