MolNFT v1 · #66108 · protein
Structural and functional studies of the yeast class II HDA1 hdac complex
3HGQ · HDA1 complex subunit 3: “Structural and functional studies of the yeast class II HDA1 hdac complex”. X-ray diffraction, 15 pockets (best druggability 0.72). MolNFT v1 #66108 on GenesisL1: 3D structure, binding sites and pockets in…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.