MolNFT v1 · #161521 · protein
The structure of schizosaccharomyces pombe PCNA in complex with an SPD1 derived peptide
6QH1 · Proliferating cell nuclear antigen: “The structure of schizosaccharomyces pombe PCNA in complex with an SPD1 derived peptide”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #161521 on GenesisL1: 3D structure…
- PDB
- 6QH1
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; S-phase delaying protein 1
- UniProt
- Q03392, Q10585
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 243 | 20% helix, 47% strand | Q03392 |
| B | Proliferating cell nuclear antigen | protein | 251 | 20% helix, 47% strand | Q03392 |
| C | Proliferating cell nuclear antigen | protein | 242 | 20% helix, 46% strand | Q03392 |
| D | S-phase delaying protein 1 | protein | 10 | 40% helix, 0% strand | Q10585 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.75 | 0.99 | 20 | empty |
| 2 | 55 | 0.74 | 0.98 | 18 | empty |
| 3 | 98 | 0.50 | 0.82 | 16 | empty |
| 4 | 122 | 0.44 | 0.77 | 19 | empty |
| 5 | 120 | 0.41 | 0.76 | 29 | empty |
Interfaces
4 interfaces between chains.
- B–C · 794 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 500 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6QH1 · The structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q03392 · AlphaFold monomer V2.0 prediction for proliferating cell nuclear antigen (Q03392) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q10585 · AlphaFold monomer V2.0 prediction for S-phase delaying protein 1 (Q10585) · a predicted model of the same protein · chain D against A, TM-score 0.37
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 Q03392
- Every structure of UniProt Q10585
- Elsewhere: RCSB PDB 6QH1 · PDBe 6QH1 · UniProt Q03392 · UniProt Q10585
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