Research workbench
The structure of schizosaccharomyces pombe PCNA in complex with an SPD1 derived peptide
Analyse The structure of schizosaccharomyces pombe PCNA in complex with an SPD1 derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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