SAXSdb — 2vcg

▼

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

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE

ALCALIGENES SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 POTASSIUM ION × 4 methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate × 2 GLYCEROL × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 POTASSIUM ION × 4 methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDAH_ALCSD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–375； UniProt 1–368 Author chain B； PDBConstruct 8–375； UniProt 1–368 Author chain C； PDBConstruct 8–375； UniProt 1–368 Author chain D； PDBConstruct 8–375； UniProt 1–368

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	2vcg
Deposition date deposition_date	2007-09-24
Structure title title	Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17
Keywords keywords	HDAH, INHIBITOR, HDAC-LIKE AMIDOHYDROLASE, HYDROLASE, HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE; HYDROLASE
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.

2vcg__assembly_1__model_1

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

Download this curve (.dat)

2vcg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vcg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.29 Å
Rg (electron density)	26.42 Å
Total Rg	27.14 Å
Atom count	5649
Residues	743
Excluded volume	99747 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vcg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vcg__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
Molecular weight formula_weight	40253.5 kDa
EC 编号 ec_number	3.5.1.-
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	12995

MHHHHHHAIGYVWNTLYGWVDTGTGSLAAANLTARMQPISHHLAHPDTKRRFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGDTGDGITMMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPGHHAPHNAAMGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVLTISLHQHLCFPPDSGYSTERGAGNGHGYNINVPLPPGSGNAAYLHAMDQVVLPALRAYRPQLIIVGSGFDASMLDPLARMMVTADGFRQMARRTIDCAADICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGGNTLLDAERAAIEEIVPLLADIR

Source Source

Source organism organism	ALCALIGENES SP.
NCBI taxonomy ID ncbi_taxonomy_id	512
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	5

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate
Molecular weight formula_weight	429.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1694

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2vcgA00
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	2vcgB00
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	2vcgC00
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	2vcgD00
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

▶

Unit-cell length a length_a	67.664 Å
Unit-cell length b length_b	93.633 Å
Unit-cell length c length_c	121.664 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	117.850 Å
R factor r_factor	0.1590
R_work r_work	0.1560
R_free r_free	0.2060

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

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

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE

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

2vcg__assembly_1__model_1

2vcg__assembly_1__model_1 | I(q)

2vcg__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

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

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE

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

2vcg__assembly_1__model_1

2vcg__assembly_1__model_1 | I(q)

2vcg__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)