Research workbench
HDAC-PC
Analyse HDAC-PC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z6F
- Type
- protein
- Length
- 2,387 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase HDA1; HDA1 complex subunit 3,HDA1 complex subunit 3; HDA1 complex…
- EC
- 3.5.1.98
- UniProt
- P53973, Q06623, Q06629
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 651 | 35% helix, 15% strand | P53973 |
| B | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 661 | 36% helix, 14% strand | P53973 |
| D | HDA1 complex subunit 3,HDA1 complex subunit 3 | protein | 534 | 64% helix, 5% strand | Q06623 |
| C | HDA1 complex subunit 2 | protein | 541 | 56% helix, 6% strand | Q06629 |
Ligands and binding sites
- 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
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.80 | 0.82 | 98 | empty |
| 2 | 378 | 0.76 | 0.86 | 38 | empty |
| 3 | 90 | 0.74 | 0.96 | 20 | empty |
| 4 | 756 | 0.74 | 0.79 | 79 | empty |
| 5 | 61 | 0.71 | 0.97 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5839 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 2358 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 2067 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1138 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6Z6F · HDAC-PC · the same entry in another collection · chain C against C, TM-score 1.00
- P53973 · AlphaFold monomer V2.0 prediction for histone deacetylase HDA1 (P53973) · a predicted model of the same protein · chain A against A, TM-score 0.83
- Q06629 · AlphaFold monomer V2.0 prediction for HDA1 complex subunit 2 (Q06629) · a predicted model of the same protein · chain C against A, TM-score 0.63
- Q06623 · AlphaFold monomer V2.0 prediction for HDA1 complex subunit 3 (Q06623) · a predicted model of the same protein · chain D against A, TM-score 0.54
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 P53973
- Every structure of UniProt Q06623
- Every structure of UniProt Q06629
- Elsewhere: RCSB PDB 6Z6F · PDBe 6Z6F · UniProt P53973 · UniProt Q06623 · UniProt Q06629
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.