MolNFT v1 · #173084 · protein
Structure of the extended MTA1/HDAC1/MBD2/RBBP4 nurd deacetylase complex
7AOA · Methyl-cpg-binding domain protein 2: “Structure of the extended MTA1/HDAC1/MBD2/RBBP4 nurd deacetylase complex”. Electron microscopy, 3 ligands (IHP, K, ZN), 20 pockets (best druggability 0.76). MolNFT v1 #173084 on GenesisL1: 3D…
- PDB
- 7AOA
- Type
- protein
- Length
- 2,258 residues
- Chains
- 7
- 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, Q09028
- Ligands
- IHP, K, ZN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 27% helix, 25% 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 | 343 | 39% helix, 16% strand | Q13330 |
| E, B | Histone deacetylase 1 (EC 3.5.1.98) | protein | 369 | 40% helix, 13% strand | Q13547 |
| F, G | Histone-binding protein RBBP4 | protein | 385 | 7% helix, 43% strand | Q09028 |
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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.76 | 0.84 | 34 | empty |
| 2 | 445 | 0.75 | 0.84 | 32 | empty |
| 3 | 226 | 0.72 | 0.87 | 33 | empty |
| 4 | 442 | 0.58 | 0.74 | 34 | empty |
| 5 | 278 | 0.58 | 0.78 | 52 | ZN |
Interfaces
7 interfaces between chains.
- A–B · 2961 Ų buried · 50 hydrogen bonds · protein-protein
- D–F · 2939 Ų buried · 38 hydrogen bonds · protein-protein
- A–G · 2937 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2936 Ų buried · 56 hydrogen bonds · protein-protein
- D–A · 1184 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7AOA · Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex · the same entry in another collection · chain G against G, 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
- Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain F against A, TM-score 0.97
- 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 0.44
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
- Every structure of UniProt Q09028
- Elsewhere: RCSB PDB 7AOA · PDBe 7AOA · UniProt Q9UBB5 · UniProt Q13330 · UniProt Q13547 · UniProt Q09028
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