Research workbench
The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 midac deacetylase complex
Analyse The structure of the dimeric 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
- 6Z2J
- Type
- protein
- Length
- 1,185 residues
- Chains
- 6
- 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, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Histone deacetylase 1 (EC 3.5.1.98) | protein | 369 | 39% helix, 10% strand | Q13547 |
| E | Histone deacetylase 1 (EC 3.5.1.98) | protein | 368 | 39% helix, 10% strand | Q13547 |
| A, B | Deoxynucleotidyltransferase terminal-interacting protein 1 | protein | 69 | 86% helix, 0% strand | Q9H147 |
| F, D | Mitotic deacetylase-associated sant domain protein | protein | 155 | 43% helix, 3% strand | Q6PJG2 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains C, D, E, F
- K · Potassium ion · metal · 4 copies · chains C, E
- ZN · Zinc ion · metal · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.78 | 0.84 | 66 | empty |
| 2 | 582 | 0.78 | 0.84 | 69 | empty |
| 3 | 242 | 0.78 | 0.90 | 38 | empty |
| 4 | 166 | 0.77 | 0.93 | 34 | empty |
| 5 | 72 | 0.71 | 0.95 | 18 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2626 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2556 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1998 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 409 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 385 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z2J · The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q13547 · AlphaFold monomer V2.0 prediction for histone deacetylase 1 (Q13547) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9H147 · AlphaFold monomer V2.0 prediction for deoxynucleotidyltransferase terminal-interacting… · a predicted model of the same protein · chain A against A, TM-score 0.92
- Q6PJG2 · AlphaFold monomer V2.0 prediction for mitotic deacetylase-associated sant domain protein… · a predicted model of the same protein · chain F against A, TM-score 0.78
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 6Z2J · PDBe 6Z2J · UniProt Q13547 · UniProt Q9H147 · UniProt Q6PJG2
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