MolNFT v1 · #15498 · protein + DNA
Structural basis of sequence-specific recruitment of histone deacetylases by myocyte enhancer factor-2
1N6J · 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3': “Structural basis of sequence-specific recruitment of histone deacetylases by myocyte enhancer factor-2”. X-ray diffraction, 5 pockets (best druggability 0.56). MolNFT v1 #15498 on…
- PDB
- 1N6J
- Type
- protein + DNA
- Length
- 237 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3'…
- UniProt
- Q02080, Q9Y6J0
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3' | dna | 14 | — | — |
| D | 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3' | dna | 14 | — | — |
| A | Myocyte-specific enhancer factor 2B | protein | 93 | 52% helix, 17% strand | Q02080 |
| B | Myocyte-specific enhancer factor 2B | protein | 90 | 49% helix, 18% strand | Q02080 |
| G | Calcineurin-binding protein cabin 1 | protein | 26 | 46% helix, 0% strand | Q9Y6J0 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.56 | 0.76 | 33 | empty |
| 2 | 69 | 0.56 | 0.89 | 19 | empty |
| 3 | 98 | 0.55 | 0.85 | 20 | empty |
| 4 | 220 | 0.48 | 0.75 | 18 | empty |
| 5 | 82 | 0.38 | 0.78 | 19 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3202 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 638 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–G · 574 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 515 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–G · 505 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1N6J · Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte… · the same entry in another collection · chain G against G, 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 B against A, TM-score 0.98
- Q9Y6J0 · AlphaFold monomer V2.0 prediction for calcineurin-binding protein cabin-1 (Q9Y6J0) · a predicted model of the same protein · chain G against A, TM-score 0.60
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 Q9Y6J0
- Elsewhere: RCSB PDB 1N6J · PDBe 1N6J · UniProt Q02080 · UniProt Q9Y6J0
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