Research workbench
The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 midac deacetylase complex
Analyse The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 midac deacetylase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z2K
- Type
- protein
- Length
- 2,379 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 1; Deoxynucleotidyltransferase terminal-interacting protein 1…
- EC
- 3.5.1.98
- UniProt
- Q13547, Q9H147, Q6PJG2
- Ligands
- IHP, K, ZN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, K, I | Histone deacetylase 1 (EC 3.5.1.98) | protein | 369 | 39% helix, 12% strand | Q13547 |
| E | Histone deacetylase 1 (EC 3.5.1.98) | protein | 368 | 39% helix, 11% strand | Q13547 |
| A, B, G, H | Deoxynucleotidyltransferase terminal-interacting protein 1 | protein | 69 | 86% helix, 0% strand | Q9H147 |
| F, D, L, J | Mitotic deacetylase-associated sant domain protein | protein | 157 | 43% helix, 3% strand | Q6PJG2 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains E, F, L, K, I, D, J, C
- K · Potassium ion · metal · 8 copies · chains C, E, K, I
- ZN · Zinc ion · metal · 4 copies · chains C, E, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.78 | 0.82 | 85 | empty |
| 2 | 614 | 0.77 | 0.83 | 70 | empty |
| 3 | 533 | 0.77 | 0.84 | 56 | empty |
| 4 | 570 | 0.76 | 0.83 | 63 | empty |
| 5 | 145 | 0.76 | 0.93 | 28 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2377 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2323 Ų buried · 35 hydrogen bonds · protein-protein
- K–L · 2305 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2298 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1953 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6Z2K · The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex · the same entry in another collection · chain J against J, 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 Q13547
- Every structure of UniProt Q9H147
- Every structure of UniProt Q6PJG2
- Elsewhere: RCSB PDB 6Z2K · PDBe 6Z2K · UniProt Q13547 · UniProt Q9H147 · UniProt Q6PJG2
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