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
- 3V61
- Type
- protein
- Length
- 331 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
- NEQ, BA
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like protein SMT3 | protein | 77 | 21% helix, 30% strand | Q12306 |
| B | Proliferating cell nuclear antigen | protein | 254 | 22% helix, 45% strand | P15873 |
Ligands and binding sites
- NEQ · N-ethylmaleimide · ligand · 2 copies · chains B
- BA · Barium ion · metal · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.61 | 0.85 | 20 | NEQ |
| 2 | 78 | 0.39 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 59 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 3V61 · 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 0.95
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 3V61 · PDBe 3V61 · UniProt Q12306 · UniProt P15873
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