Research workbench
Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated daxx
Analyse Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated daxx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYX
- Type
- protein
- Length
- 174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small ubiquitin-related modifier 1; Phosphorylated daxx
- UniProt
- P63165
- Ligands
- SEP
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Small ubiquitin-related modifier 1 | protein | 79 | 23% helix, 34% strand | P63165 |
| D | Phosphorylated daxx | protein | 8 | 0% helix, 38% strand | — |
| A | Small ubiquitin-related modifier 1 | protein | 77 | 23% helix, 35% strand | P63165 |
| B | Phosphorylated daxx | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
- SEP · Phosphoserine · ligand · chains C, D
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 | 80 | 0.42 | 0.80 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 610 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 461 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 340 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 331 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (acetylation, covalent ligand, phosphorylation).
Compared structures
- 6UYX · Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated DAXX · the same entry in another collection · chain C against C, TM-score 1.00
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P63165
- Elsewhere: RCSB PDB 6UYX · PDBe 6UYX · UniProt P63165
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