SAXSdb — 6z6f

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

Histone deacetylase HDA1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA1_YEAST
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–661； UniProt 40–700 Author chain B； PDBConstruct 1–672； UniProt 29–700

HDA1 complex subunit 3,HDA1 complex subunit 3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06623

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 2 × 1 （Q06629） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–307； UniProt 28–334 Author chain D； PDBConstruct 308–543； UniProt 404–639

HDA1 complex subunit 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06629

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–629； UniProt 10–638

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	6z6f
Deposition date deposition_date	2020-05-28
Structure title title	HDAC-PC
Keywords keywords	Protein complex, GENE REGULATION; GENE REGULATION
Experimental Method method	ELECTRON MICROSCOPY

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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.

6z6f__assembly_1__model_1

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

Download this curve (.dat)

6z6f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z6f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.48 Å
Rg (electron density)	52.66 Å
Total Rg	52.66 Å
Atom count	19217
Residues	2387
Excluded volume	342920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z6f__assembly_1__model_1`	tetrameric （4）	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	Histone deacetylase HDA1
Molecular weight formula_weight	74852.0 kDa
EC 编号 ec_number	3.5.1.98
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	19217

RQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFEYIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATSEEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPCGGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNILKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPGTIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKPDLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGYNLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYWNCFRRRHANSGCNFNEPINDSIISKNFPLQKAIRQQQQHYLSDEFNFVTLPLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSSVIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWDNYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLKPLVPLVDETLSEWYFKNSLIFSNNSHQCWKENESRKPRKKFGRVLRCDTDGLNNIIEERFEEATDFILDSFE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone deacetylase HDA1
Molecular weight formula_weight	76017.2 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ENSLSTTSKSKRQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFEYIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATSEEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPCGGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNILKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPGTIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKPDLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGYNLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYWNCFRRRHANSGCNFNEPINDSIISKNFPLQKAIRQQQQHYLSDEFNFVTLPLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSSVIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWDNYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLKPLVPLVDETLSEWYFKNSLIFSNNSHQCWKENESRKPRKKFGRVLRCDTDGLNNIIEERFEEATDFILDSFE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	HDA1 complex subunit 3,HDA1 complex subunit 3
Molecular weight formula_weight	63422.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SGDYWLPTTMSLYQKELTDQIVSLHYSDILRYFETSHYKEDVILESMKTMCLNGSLVATHPYLLIDHYMPKSLITRDVPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSKQKANDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKFDKNSREYLENVTAAMVILRDRLGTLPPDLRPIYSQKLHYLVEWLENPTVPWPLPDIYPLKQYTSMDVERSLLTEVHFKKNSSNVNYHLSSGIITHKLIQSMGEVYMDICVQKQELDDYSCLDDLQNDHLKFFSNEDEKIIKEYETVLRTNNENLNRSHELEVENNLKFSQIETLEKDIETLKGSLMAQGETLSKLKDAFVKTDNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKFEKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENLTIPRVRTQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	HDA1 complex subunit 2
Molecular weight formula_weight	71915.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KVYYLPVTLTQFQKDLSEILISLHAKSFKASIIGEPQADAVNKPSGLPAGPETHPYPTLSQRQLTYIFDSNIRAIANHPSLLVDHYMPRQLLRMEPTESSIAGSHKFQVLNQLINSICFRDREGSPNEVIKCAIIAHSIKELDLLEGLILGKKFRTKRLSGTSLYNEKHKFPNLPTVDSTINKDGTPNSVSSTSSNSNSTSYTGYSKDDYDYSVKRNLKKRKINTDDWLFLATTKHLKHDQYLLANYDIDMIISFDPMLEVELPALQVLRNNANKDIPIIKLLVQNSPDHYLLDSEIKNSSVKSSHLSNNGHVDDSQEYEEIKSSLLYFLQARNAPVNNCEIDYIKLVKCCLEGKDCNNILPVLDLITLDEASKDSSDSGFWQPQLTKLQYSSTELPLWDGPLDIKTYQTELMHRAVIRLRDIQDEYAKGTVPLYEKRLNETQRQNQLDEIKNSVGLTFKKKQEVEKSINDSEKRLKHAMTESTKLQNKINHLLKNRQELENFNKLPSNTISSENHLEEGSALADKLKEYIDKNATLFNKLKELQQANAEKSKLNDELRSKYQIESSKAAESAQTLKILQESMKSLENEVNGPLTKFSTESLKKELERLQNDFQSLKARNKFLKNYITL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6z6fA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6fB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6fD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12360 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.11 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	466972

HDAC-PC

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

Histone deacetylase HDA1

State in the Current Structure

Other States of the Same Protein in the Database

HDA1 complex subunit 3,HDA1 complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

HDA1 complex subunit 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

6z6f__assembly_1__model_1

6z6f__assembly_1__model_1 | I(q)

6z6f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

HDAC-PC

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

Histone deacetylase HDA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HDA1 complex subunit 3,HDA1 complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HDA1 complex subunit 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

6z6f__assembly_1__model_1

6z6f__assembly_1__model_1 | I(q)

6z6f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)