Research workbench
Structure of the Y246A mutant of the panton-valentine leucocidin S component from staphylococcus aureus
Analyse Structure of the Y246A mutant of the panton-valentine leucocidin S component… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J0O
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luks-pv
- UniProt
- O80066
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luks-pv | protein | 275 | 4% helix, 64% strand | O80066 |
| B | Luks-pv | protein | 277 | 4% helix, 65% strand | O80066 |
| C | Luks-pv | protein | 275 | 4% helix, 64% strand | O80066 |
| D | Luks-pv | protein | 272 | 4% helix, 65% strand | O80066 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.80 | 0.81 | 90 | empty |
| 2 | 903 | 0.77 | 0.80 | 80 | empty |
| 3 | 170 | 0.42 | 0.74 | 28 | empty |
| 4 | 62 | 0.41 | 0.80 | 22 | empty |
| 5 | 58 | 0.40 | 0.81 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 565 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 287 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 276 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4J0O · Structure of the Y246A Mutant of the PANTON-VALENTINE LEUCOCIDIN S Component from… · 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 O80066
- Elsewhere: RCSB PDB 4J0O · PDBe 4J0O · UniProt O80066
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