SAXSdb — 3phd

▼

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

Histone deacetylase 6

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Polyubiquitin × 4 （P62988） ZINC ION × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDAC6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 1109–1215 Author chain B； PDBConstruct 1–107； UniProt 1109–1215 Author chain C； PDBConstruct 1–107； UniProt 1109–1215 Author chain D； PDBConstruct 1–107； UniProt 1109–1215

Polyubiquitin

Homo sapiens

UniProt P62988

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Histone deacetylase 6 × 4 （Q9UBN7） ZINC ION × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3phd
Deposition date deposition_date	2010-11-03
Structure title title	Crystal structure of human HDAC6 in complex with ubiquitin
Keywords keywords	HDAC6, ubiquitin, Structural Genomics, Structural Genomics Consortium, SGC, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3phd__assembly_1__model_1

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

Download this curve (.dat)

3phd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3phd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.33 Å
Rg (electron density)	23.15 Å
Total Rg	23.78 Å
Atom count	3319
Residues	469
Excluded volume	57280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3phd__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Histone deacetylase 6
Molecular weight formula_weight	12023.7 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3321

PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPHPH

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 polymer

Description description	Polyubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3phdf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id	3phdA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3phdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3phdC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3phdD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

▶

Unit-cell length a length_a	133.748 Å
Unit-cell length b length_b	133.748 Å
Unit-cell length c length_c	118.768 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	32.720 Å
R factor r_factor	0.2352
R_work r_work	0.2346
R_free r_free	0.2648

Crystal structure of human HDAC6 in complex with ubiquitin

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

Histone deacetylase 6

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin

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

3phd__assembly_1__model_1

3phd__assembly_1__model_1 | I(q)

3phd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human HDAC6 in complex with ubiquitin

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

Histone deacetylase 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin

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

3phd__assembly_1__model_1

3phd__assembly_1__model_1 | I(q)

3phd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)