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3gv4

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

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 6

Homo sapiens

UniProt Q9UBN7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 ubiquitin C-terminal peptide RLRGG × 1 ZINC ION × 3 CALCIUM ION × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3c5k 5b8d 5kh3 5kh7 5kh9 5wbn 5wpb 6ce6 6ce8 6cea 6cec 6ced

17 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3gv4 3phd 5edu 5edu 7zyu

5 assemblies

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_id3gv4
Deposition date deposition_date2009-03-30
Structure title titleCrystal 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 methodX-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.

3gv4__assembly_1__model_1

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

Download this curve (.dat)

3gv4__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3gv4__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）13.59 Å
Rg (electron density)12.45 Å
Total Rg13.70 Å
Atom count803
Residues103
Excluded volume14280 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3gv4__assembly_1__model_1 dimeric （2） 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)

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3gv4A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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7. Citations (1)