Research workbench
Crystal structure of daxx N-terminal four-helix bundle domain (4HB) in complex with atrx
Analyse Crystal structure of daxx N-terminal four-helix bundle domain (4HB) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y6O
- Type
- protein
- Length
- 947 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx
- EC
- 3.6.4.12
- UniProt
- Q9UER7, P46100
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 105 | 76% helix, 0% strand | Q9UER7, P46100 |
| B | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 105 | 76% helix, 2% strand | Q9UER7, P46100 |
| C | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 106 | 71% helix, 0% strand | Q9UER7, P46100 |
| D, E | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 108 | 73% helix, 0% strand | Q9UER7, P46100 |
| F | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 104 | 75% helix, 0% strand | Q9UER7, P46100 |
| G | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 105 | 72% helix, 0% strand | Q9UER7, P46100 |
| H | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 103 | 81% helix, 0% strand | Q9UER7, P46100 |
| I | Death domain-associated protein 6,TRANSCRIPTIONAL regulator atrx (EC 3.6.4.12) | protein | 103 | 74% helix, 0% strand | Q9UER7, P46100 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.79 | 0.81 | 106 | empty |
| 2 | 325 | 0.72 | 0.84 | 41 | empty |
| 3 | 342 | 0.68 | 0.82 | 46 | empty |
| 4 | 546 | 0.63 | 0.75 | 50 | empty |
| 5 | 298 | 0.55 | 0.75 | 31 | empty |
Interfaces
15 interfaces between chains.
- G–I · 906 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 873 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 872 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 866 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5Y6O · Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX · the same entry in another collection · chain I against I, TM-score 1.00
- Q9UER7 · AlphaFold monomer V2.0 prediction for death domain-associated protein 6 (Q9UER7) · a predicted model of the same protein · chain F against A, TM-score 0.79
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 Q9UER7
- Every structure of UniProt P46100
- Elsewhere: RCSB PDB 5Y6O · PDBe 5Y6O · UniProt Q9UER7 · UniProt P46100
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