Research workbench
Structure of S. cerevisiae PCNA conjugated to sumo on lysine 164
Analyse Structure of S. cerevisiae PCNA conjugated to sumo on lysine 164 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V60
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein SMT3; Proliferating cell nuclear antigen
- UniProt
- Q12306, P15873
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like protein SMT3 | protein | 79 | 14% helix, 33% strand | Q12306 |
| B | Proliferating cell nuclear antigen | protein | 256 | 19% helix, 46% strand | P15873 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.36 | 0.76 | 17 | empty |
| 2 | 75 | 0.35 | 0.76 | 19 | empty |
| 3 | 50 | 0.24 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3V60 · Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 · the same entry in another collection · chain A against A, TM-score 1.00
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q12306
- Every structure of UniProt P15873
- Elsewhere: RCSB PDB 3V60 · PDBe 3V60 · UniProt Q12306 · UniProt P15873
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