Research workbench
Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated pml-sim
Analyse Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated pml-sim in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYU
- Type
- protein
- Length
- 176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small ubiquitin-related modifier 1; Protein pml
- UniProt
- P63165, P29590
- Ligands
- SEP
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small ubiquitin-related modifier 1 | protein | 79 | 23% helix, 34% strand | P63165 |
| B | Protein pml | protein | 11 | 0% helix, 27% strand | P29590 |
| C | Small ubiquitin-related modifier 1 | protein | 76 | 24% helix, 36% strand | P63165 |
| D | Protein pml | protein | 10 | 0% helix, 30% strand | P29590 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 2 copies · chains A, B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.60 | 0.83 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 578 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 569 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 covalent (phosphorylation, covalent ligand, acetylation).
Compared structures
- 6UYU · Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.98
- P29590 · AlphaFold monomer V2.0 prediction for protein pml (P29590) · a predicted model of the same protein · chain D against A, TM-score 0.44
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
- Every structure of UniProt P29590
- Elsewhere: RCSB PDB 6UYU · PDBe 6UYU · UniProt P63165 · UniProt P29590
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