MolNFT v1 · #171482 · protein
HDAC-TC
6Z6O · Histone deacetylase HDA1: “HDAC-TC”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #171482 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z6O
- Type
- protein
- Length
- 9,628 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase HDA1; HDA1 complex subunit 2; HDA1 complex subunit 3,HDA1 complex…
- EC
- 3.5.1.98
- UniProt
- P53973, Q06629, Q06623
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 656 | 36% helix, 15% strand | P53973 |
| B, F, J, N | Histone deacetylase HDA1 (EC 3.5.1.98) | protein | 661 | 35% helix, 15% strand | P53973 |
| C, G, K, O | HDA1 complex subunit 2 | protein | 548 | 55% helix, 6% strand | Q06629 |
| D, H, L, P | HDA1 complex subunit 3,HDA1 complex subunit 3 | protein | 542 | 63% helix, 6% strand | Q06623 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F, I, J, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.86 | 0.87 | 132 | empty |
| 2 | 956 | 0.86 | 0.87 | 136 | empty |
| 3 | 1163 | 0.84 | 0.85 | 142 | empty |
| 4 | 1120 | 0.81 | 0.82 | 101 | empty |
| 5 | 532 | 0.81 | 0.87 | 67 | empty |
Interfaces
36 interfaces between chains.
- E–F · 5465 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 5460 Ų buried · 38 hydrogen bonds · protein-protein
- M–N · 5454 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 5444 Ų buried · 37 hydrogen bonds · protein-protein
- J–K · 2506 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6Z6O · HDAC-TC · the same entry in another collection · chain K against K, 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 P53973
- Every structure of UniProt Q06629
- Every structure of UniProt Q06623
- Elsewhere: RCSB PDB 6Z6O · PDBe 6Z6O · UniProt P53973 · UniProt Q06629 · UniProt Q06623
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