MolNFT v1 · #166716 · protein
Crystal structure of K37-acetylated SUMO1 in complex with pml-sim
6UYO · Small ubiquitin-related modifier 1: “Crystal structure of K37-acetylated SUMO1 in complex with pml-sim”. X-ray diffraction, 1 pocket (best druggability 0.29). MolNFT v1 #166716 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6UYO
- Type
- protein
- Length
- 172 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
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small ubiquitin-related modifier 1 | protein | 75 | 24% helix, 36% strand | P63165 |
| B | Protein pml | protein | 12 | 0% helix, 25% strand | P29590 |
| C | Small ubiquitin-related modifier 1 | protein | 76 | 24% helix, 36% strand | P63165 |
| D | Protein pml | protein | 9 | 0% helix, 33% strand | P29590 |
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 | 50 | 0.29 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 603 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 482 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 6UYO · Crystal structure of K37-acetylated SUMO1 in complex with 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 A 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 0.48
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 6UYO · PDBe 6UYO · UniProt P63165 · UniProt P29590
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