Research workbench
Crystal structure of dhb domain of daxx in complex with an atrx peptide
Analyse Crystal structure of dhb domain of daxx in complex with an atrx peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GRQ
- Type
- protein
- Length
- 231 residues
- Chains
- 4
- 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
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death domain-associated protein 6 | protein | 90 | 72% helix, 2% strand | Q9UER7 |
| B | Death domain-associated protein 6 | protein | 85 | 76% helix, 2% strand | Q9UER7 |
| C | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 30 | 53% helix, 0% strand | P46100 |
| D | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 26 | 73% helix, 0% strand | P46100 |
Ligands and binding sites
- ZN · Zinc ion · metal · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.40 | 0.76 | 27 | CL |
Interfaces
3 interfaces between chains.
- A–C · 850 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 679 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 494 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5GRQ · Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.97
- P46100 · AlphaFold monomer V2.0 prediction for transcriptional regulator atrx (P46100) · a predicted model of the same protein · chain D against A, TM-score 0.66
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 5GRQ · PDBe 5GRQ · UniProt Q9UER7 · UniProt P46100
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