Research workbench
Ideal thiolate-zinc coordination geometry in depsipeptide binding to histone deacetylase 8
Analyse Ideal thiolate-zinc coordination geometry in depsipeptide binding to histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RQD
- Type
- protein
- Length
- 718 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Largazole
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- 02G, K, ZN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 354 | 41% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 356 | 40% helix, 13% strand | Q9BY41 |
| C, D | Largazole | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 02G · (3S,4E)-3-hydroxy-7-sulfanylhept-4-enoic acid · ligand · 2 copies · chains A, C, B, D
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.72 | 0.90 | 35 | empty |
| 2 | 234 | 0.61 | 0.80 | 44 | empty |
| 3 | 126 | 0.38 | 0.74 | 40 | empty |
| 4 | 54 | 0.27 | 0.74 | 11 | empty |
| 5 | 66 | 0.27 | 0.72 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 644 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 194 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 175 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 3RQD · Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9BY41
- Elsewhere: RCSB PDB 3RQD · PDBe 3RQD · UniProt Q9BY41
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