MolNFT v1 · #86909 · protein
The structure of HDAC1 in complex with the dimeric ELM2-sant domain of MTA1 from the nurd complex
4BKX · Metastasis-associated protein MTA1: “The structure of HDAC1 in complex with the dimeric ELM2-sant domain of MTA1 from the nurd complex”. X-ray diffraction, 3 ligands (K, ZN, SO4), 5 pockets (best druggability 0.55). MolNFT v1 #86909…
- PDB
- 4BKX
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metastasis-associated protein MTA1; Histone deacetylase 1
- EC
- 3.5.1.98
- UniProt
- Q13330, Q13547
- Ligands
- K, ZN, SO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metastasis-associated protein MTA1 | protein | 161 | 52% helix, 3% strand | Q13330 |
| B | Histone deacetylase 1 (EC 3.5.1.98) | protein | 369 | 39% helix, 13% strand | Q13547 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains B
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains B, A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.55 | 0.78 | 27 | empty |
| 2 | 90 | 0.41 | 0.78 | 14 | SO4 |
| 3 | 62 | 0.39 | 0.80 | 19 | empty |
| 4 | 120 | 0.37 | 0.74 | 25 | empty |
| 5 | 74 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2733 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4BKX · The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13547 · AlphaFold monomer V2.0 prediction for histone deacetylase 1 (Q13547) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13330 · AlphaFold monomer V2.0 prediction for metastasis-associated protein MTA1 (Q13330) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q13330
- Every structure of UniProt Q13547
- Elsewhere: RCSB PDB 4BKX · PDBe 4BKX · UniProt Q13330 · UniProt Q13547
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