MolNFT v1 · #116327 · protein
Monomeric PCNA bound to a small protein inhibitor
5DA7 · DNA polymerase sliding clamp 1, proliferating cell nuclear…: “Monomeric PCNA bound to a small protein inhibitor”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.75). MolNFT v1 #116327 on GenesisL1: 3D structure…
- PDB
- 5DA7
- Type
- protein
- Length
- 564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp 1, proliferating cell nuclear antigen; Thermococcales…
- UniProt
- Q5JF32, Q5JH72
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase sliding clamp 1, proliferating cell nuclear antigen | protein | 247 | 17% helix, 46% strand | Q5JF32 |
| B, E | Thermococcales inhibitor of PCNA | protein | 35 | 54% helix, 6% strand | Q5JH72 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.75 | 0.83 | 42 | SO4 |
| 2 | 63 | 0.56 | 0.88 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1528 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1503 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 725 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 120 Ų buried · 1 hydrogen bond · protein-protein
- D–B · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DA7 · monomeric PCNA bound to a small protein inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JF32 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (Q5JF32) · a predicted model of the same protein · chain A against A, TM-score 0.85
- Q5JH72 · AlphaFold monomer V2.0 prediction for PCNA-inhibitor (Q5JH72) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 Q5JF32
- Every structure of UniProt Q5JH72
- Elsewhere: RCSB PDB 5DA7 · PDBe 5DA7 · UniProt Q5JF32 · UniProt Q5JH72
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