MolNFT v1 · #85238 · protein
Structure of HDAC3 bound to corepressor and inositol tetraphosphate
4A69 · Histone deacetylase 3,: “Structure of HDAC3 bound to corepressor and inositol tetraphosphate”. X-ray diffraction, 3 ligands (I0P, K, ZN), 7 pockets (best druggability 0.84). MolNFT v1 #85238 on GenesisL1: 3D structure, binding sites…
- PDB
- 4A69
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 3,; Nuclear receptor corepressor 2
- EC
- 3.5.1.98
- UniProt
- O15379, Q9Y618
- Ligands
- I0P, K, ZN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase 3, (EC 3.5.1.98) | protein | 369 | 40% helix, 13% strand | O15379 |
| C | Nuclear receptor corepressor 2 | protein | 69 | 58% helix, 4% strand | Q9Y618 |
| D | Nuclear receptor corepressor 2 | protein | 68 | 59% helix, 4% strand | Q9Y618 |
Ligands and binding sites
- I0P · D-myo inositol 1,4,5,6 tetrakisphosphate · ligand · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.84 | 0.89 | 99 | empty |
| 2 | 388 | 0.76 | 0.86 | 35 | GOL, I0P |
| 3 | 89 | 0.56 | 0.86 | 27 | empty |
| 4 | 142 | 0.51 | 0.80 | 20 | empty |
| 5 | 63 | 0.35 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1198 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1178 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 806 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 190 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4A69 · Structure of HDAC3 bound to corepressor and inositol tetraphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- O15379 · AlphaFold monomer V2.0 prediction for histone deacetylase 3 (O15379) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain C against A, TM-score 0.70
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 O15379
- Every structure of UniProt Q9Y618
- Elsewhere: RCSB PDB 4A69 · PDBe 4A69 · UniProt O15379 · UniProt Q9Y618
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