Research workbench
Structure of PCNA bound to a small molecule inhibitor
Analyse Structure of PCNA bound to a small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WGW
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen
- UniProt
- P12004
- Ligands
- T2B, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 248 | 19% helix, 46% strand | P12004 |
| B | Proliferating cell nuclear antigen | protein | 249 | 19% helix, 48% strand | P12004 |
Ligands and binding sites
- T2B · 4-{4-[(2S)-2-amino-3-hydroxypropyl]-2,6-diiodophenoxy}phenol · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.72 | 0.78 | 57 | T2B |
| 2 | 89 | 0.46 | 0.80 | 19 | empty |
| 3 | 84 | 0.35 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 453 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3WGW · Structure of PCNA bound to a small molecule inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 P12004
- Elsewhere: RCSB PDB 3WGW · PDBe 3WGW · UniProt P12004
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