Research workbench
Structural and functional studies of the yeast class II HDA1 hdac complex
Analyse Structural and functional studies of the yeast class II HDA1 hdac complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HGQ
- Type
- protein
- Length
- 1,169 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDA1 complex subunit 3
- UniProt
- Q06623
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDA1 complex subunit 3 | protein | 299 | 41% helix, 12% strand | Q06623 |
| B, C, D | HDA1 complex subunit 3 | protein | 290 | 43% helix, 12% strand | Q06623 |
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.72 | 0.77 | 72 | empty |
| 2 | 1163 | 0.72 | 0.76 | 77 | empty |
| 3 | 467 | 0.64 | 0.77 | 44 | empty |
| 4 | 272 | 0.53 | 0.76 | 43 | empty |
| 5 | 270 | 0.53 | 0.75 | 42 | empty |
Interfaces
4 interfaces between chains.
- C–D · 875 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 872 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3HGQ · Structural and functional studies of the yeast class II Hda1 HDAC complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q06623 · AlphaFold monomer V2.0 prediction for HDA1 complex subunit 3 (Q06623) · a predicted model of the same protein · chain B 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 Q06623
- Elsewhere: RCSB PDB 3HGQ · PDBe 3HGQ · UniProt Q06623
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