Research workbench
Crystal structure of SWI5-SFR1 complex from fission yeast
Analyse Crystal structure of SWI5-SFR1 complex from fission yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VIQ
- Type
- protein
- Length
- 393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SWI5-dependent recombination DNA repair protein 1; Mating-type switching protein SWI5
- UniProt
- Q9USV1, Q9UUB7
- Ligands
- NO3, SO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SWI5-dependent recombination DNA repair protein 1 | protein | 122 | 58% helix, 13% strand | Q9USV1 |
| B | Mating-type switching protein SWI5 | protein | 85 | 79% helix, 0% strand | Q9UUB7 |
| C | SWI5-dependent recombination DNA repair protein 1 | protein | 116 | 57% helix, 12% strand | Q9USV1 |
| D | Mating-type switching protein SWI5 | protein | 70 | 71% helix, 0% strand | Q9UUB7 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · chains A, B
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 7 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.57 | 0.75 | 36 | empty |
| 2 | 160 | 0.54 | 0.79 | 20 | empty |
| 3 | 190 | 0.51 | 0.77 | 29 | GOL |
| 4 | 55 | 0.29 | 0.75 | 10 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 2260 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1937 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1063 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3VIQ · Crystal structure of Swi5-Sfr1 complex from fission yeast · the same entry in another collection · chain D against D, TM-score 1.00
- Q9USV1 · AlphaFold monomer V2.0 prediction for SWI5-dependent recombination DNA repair protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9UUB7 · AlphaFold monomer V2.0 prediction for mating-type switching protein SWI5 (Q9UUB7) · a predicted model of the same protein · chain D against A, TM-score 0.65
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 Q9USV1
- Every structure of UniProt Q9UUB7
- Elsewhere: RCSB PDB 3VIQ · PDBe 3VIQ · UniProt Q9USV1 · UniProt Q9UUB7
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