SAXSdb — 3gv4

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

Histone deacetylase 6

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1109–1215	Fragment：UNP residues 1109-1215	ubiquitin C-terminal peptide RLRGG × 1 ZN ZINC ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；297 K；20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.72 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3GV4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C5K Crystal structure of human HDAC6 zinc finger domain Deposited 2008-01-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1215（107 aa） Fragment：Residues 1109-1215	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；3.5M Na formate, 100mM Bis-tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.55 Å R-free 0.227
3PHD Crystal structure of human HDAC6 in complex with ubiquitin Deposited 2010-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1109–1215（107 aa） Chain B 1109–1215（107 aa） Chain C 1109–1215（107 aa） Chain D 1109–1215（107 aa）	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；297 K；15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K	Resolution 3.00 Å R-free 0.265
5B8D Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 FMT FORMIC ACID × 2 6T4 ~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide × 1 UNX UNKNOWN LIGAND × 36 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.05 Å R-free 0.146
5EDU Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A Deposited 2015-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 479–835（357 aa） Fragment：MBP + HD6 catalytic domain 2 (UNP residues 479-835)	Not recorded	TSN TRICHOSTATIN A × 1 ZN ZINC ION × 1 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate, 20% PEG3350	Resolution 2.79 Å R-free 0.275
5EDU Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A Deposited 2015-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 479–835（357 aa） Fragment：MBP + HD6 catalytic domain 2 (UNP residues 479-835)	Not recorded	TSN TRICHOSTATIN A × 1 ZN ZINC ION × 1 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate, 20% PEG3350	Resolution 2.79 Å R-free 0.275
5KH3 Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 13 6U6 3-(5-chloranyl-1,3-benzothiazol-2-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.60 Å R-free 0.191
5KH7 Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 6T7 3-(6-oxidanylidene-3-pyridin-3-yl-pyridazin-1-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.70 Å R-free 0.183
5KH9 Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 FMT FORMIC ACID × 1 6T5 6-methyl-5-[(4-propan-2-ylphenyl)amino]-2~{H}-1,2,4-triazin-3-one × 1 UNX UNKNOWN LIGAND × 33 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.07 Å R-free 0.150
5WBN Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2017-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1108–1213（106 aa）	Not recorded	ZN ZINC ION × 3 9ZV 3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 8 FMT FORMIC ACID × 3 CL CHLORIDE ION × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.64 Å R-free 0.168
5WPB Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2017-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 957–1056（100 aa）	Not recorded	ZN ZINC ION × 3 B8P 3-{3-[(pyridin-2-yl)methoxy]quinoxalin-2-yl}propanoic acid × 1 UNX UNKNOWN LIGAND × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol	Resolution 1.55 Å R-free 0.162
6CE6 Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYP 3,3'-(benzo[1,2-d:5,4-d']bis[1,3]thiazole-2,6-diyl)dipropanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.60 Å R-free 0.196
6CE8 Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 4 EYV (1,3-benzothiazol-2-yl)acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.55 Å R-free 0.168
6CEA Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYY 3-(quinolin-2-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.60 Å R-free 0.198
6CEC Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 5 EY7 3-(3-methoxyquinoxalin-2-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.55 Å R-free 0.186
6CED Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 EYA 3-(3-methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.70 Å R-free 0.191
6CEE Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 EYM 3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.55 Å R-free 0.169
6CEF Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYJ 3-(1,3-benzothiazol-2-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol	Resolution 1.80 Å R-free 0.181
7ZYU HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10 Deposited 2022-05-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1108–1215（108 aa）	Not recorded	ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；3.6 M sodium formate, Bis-Tris 0.1M pH=6.7, 10% w/v Glycerol, 30% w/v 1,8-Diaminooctane(additive).	Resolution 2.43 Å R-free 0.250
8G43 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid Deposited 2023-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 ZU6 3-{3-[2-(methylamino)-2-oxoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol	Resolution 1.55 Å R-free 0.177
8G44 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(benzylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid Deposited 2023-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 ZU9 3-{3-[2-(benzylamino)-2-oxoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol	Resolution 1.55 Å R-free 0.193
8G45 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe Deposited 2023-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1109–1213（105 aa）	Not recorded	ZN ZINC ION × 3 ZUE 3-[8-chloro-3-(2-{[(2-methoxyphenyl)methyl]amino}-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl]propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol	Resolution 1.62 Å R-free 0.190

20 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

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

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	3gv4
Deposition date deposition_date	2009-03-30
Structure title title	Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG
Keywords keywords	;HDAC6, zinc finger, ubiquitin C-terminal peptide RLRGG, SGC, Actin-binding, Chromatin regulator, Cytoplasm, Hydrolase, Metal-binding, Nucleus, Phosphoprotein, Polymorphism, Repressor, Transcription, Transcription regulation, Ubl conjugation, Zinc, Zinc-finger, Structural Genomics, Structural Genomics Consortium ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.59 Å
Radius of gyration Rg (electron density) rg_electron	12.45 Å
Forward intensity I(0) i0	3002080.00
Molecular weight molecular_weight	11632.0 kDa
Excluded volume excluded_volume	14280 Å³
Envelope volume envelope_volume	15343 Å³
Hydration-shell volume shell_volume	10516 Å³
Envelope diameter envelope_diameter	38.4 Å
Shell Rg shell_rg	18.16 Å
Envelope Rg envelope_rg	12.69 Å
Shape Rg shape_rg	12.45 Å
Total Rg total_rg	13.70 Å
Total atoms total_atoms	803
Residues n_residues	103
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	41.7 Å
Rg (real space) rg_real	13.49 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	3.0020e+06
I(0) uncertainty (real space) i0_real_error	2.6430e+04
Rg (reciprocal space) rg_reciprocal	13.50 Å
I(0) (reciprocal space) i0_reciprocal	3002000.0000
Solution quality estimate total_estimate	0.9035
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.9 Å
Skewness Skewness skewness	0.070
Kurtosis Kurtosis kurtosis	-0.457
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	394400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1008

PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPHPH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ubiquitin C-terminal peptide RLRGG
Molecular weight formula_weight	559.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

RLRGG

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	3

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	205

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3gv4A00
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)

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8. Citations (1)

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Unit-cell length a length_a	31.657 Å
Unit-cell length b length_b	36.093 Å
Unit-cell length c length_c	88.998 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	33.450 Å
R factor r_factor	0.1769
R_work r_work	0.1738
R_free r_free	0.2303

fit	/app/data/saxs_computation/gv/3gv4/3gv4.fit
pddf	/app/data/pr_computation/gv/3gv4/3gv4.pr.out
profile	/app/data/saxs_computation/gv/3gv4/3gv4.dat

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)