Research workbench
Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2
Analyse Mechanism of recruitment of class II histone deacetylases by myocyte enhancer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TQE
- Type
- protein + DNA
- Length
- 474 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MEF2 binding site of NUR77 promoter; Myocyte-specific enhancer factor 2B; Histone…
- UniProt
- Q02080, Q99N13
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | MEF2 binding site of NUR77 promoter | dna | 17 | — | — |
| D, F | MEF2 binding site of NUR77 promoter | dna | 17 | — | — |
| P, Q, R, S | Myocyte-specific enhancer factor 2B | protein | 90 | 48% helix, 13% strand | Q02080 |
| X, Y | Histone deacetylase 9 | protein | 23 | 48% helix, 0% strand | Q99N13 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.66 | 0.76 | 41 | empty |
| 2 | 602 | 0.65 | 0.75 | 37 | empty |
| 3 | 414 | 0.61 | 0.76 | 37 | empty |
| 4 | 414 | 0.59 | 0.75 | 30 | empty |
| 5 | 92 | 0.54 | 0.85 | 20 | empty |
Interfaces
21 interfaces between chains.
- R–S · 3184 Ų buried · 39 hydrogen bonds · protein-protein
- P–Q · 3118 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 744 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–D · 711 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- Q–X · 650 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1TQE · Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2 · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q02080 · AlphaFold monomer V2.0 prediction for myocyte-specific enhancer factor 2B (Q02080) · a predicted model of the same protein · chain P against A, TM-score 0.96
- Q99N13 · AlphaFold monomer V2.0 prediction for histone deacetylase 9 (Q99N13) · a predicted model of the same protein · chain X against A, TM-score 0.45
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 Q02080
- Every structure of UniProt Q99N13
- Elsewhere: RCSB PDB 1TQE · PDBe 1TQE · UniProt Q02080 · UniProt Q99N13
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