MolNFT v1 · #173083 · protein
Structure of the core MTA1/HDAC1/MBD2 nurd deacetylase complex
7AO9 · Methyl-cpg-binding domain protein 2: “Structure of the core MTA1/HDAC1/MBD2 nurd deacetylase complex”. Electron microscopy, 3 ligands (IHP, K, ZN), 13 pockets (best druggability 0.73). MolNFT v1 #173083 on GenesisL1: 3D structure…
- PDB
- 7AO9
- Type
- protein
- Length
- 1,138 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 2; Metastasis-associated protein MTA1; Histone…
- EC
- 3.5.1.98
- UniProt
- Q9UBB5, Q13330, Q13547
- Ligands
- IHP, K, ZN
- Pockets
- 13 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Methyl-cpg-binding domain protein 2 | protein | 64 | 17% helix, 25% strand | Q9UBB5 |
| D, A | Metastasis-associated protein MTA1 | protein | 168 | 52% helix, 3% strand | Q13330 |
| E, B | Histone deacetylase 1 (EC 3.5.1.98) | protein | 369 | 40% helix, 13% strand | Q13547 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains D, E, A, B
- K · Potassium ion · metal · 4 copies · chains E, B
- ZN · Zinc ion · metal · 2 copies · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.73 | 0.88 | 33 | empty |
| 2 | 323 | 0.57 | 0.76 | 54 | empty |
| 3 | 237 | 0.55 | 0.77 | 24 | empty |
| 4 | 245 | 0.54 | 0.77 | 24 | empty |
| 5 | 192 | 0.48 | 0.76 | 32 | IHP |
Interfaces
5 interfaces between chains.
- D–E · 2721 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2710 Ų buried · 47 hydrogen bonds · protein-protein
- D–A · 1189 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 543 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 267 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7AO9 · Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex · the same entry in another collection · chain B against B, 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
- Q9UBB5 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 2 (Q9UBB5) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q13330 · AlphaFold monomer V2.0 prediction for metastasis-associated protein MTA1 (Q13330) · a predicted model of the same protein · chain D 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 Q9UBB5
- Every structure of UniProt Q13330
- Every structure of UniProt Q13547
- Elsewhere: RCSB PDB 7AO9 · PDBe 7AO9 · UniProt Q9UBB5 · UniProt Q13330 · UniProt Q13547
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