Research workbench
Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
Analyse Structure-based discovery of a novel small-molecule inhibitor of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U3Y
- Type
- protein
- Length
- 816 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Panton-valentine leucocidin F; Gamma-hemolysin subunit a
- UniProt
- Q5FBD2, B1Q017
- Ligands
- PQJ, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Panton-valentine leucocidin F | protein | 291 | 3% helix, 58% strand | Q5FBD2 |
| B | Gamma-hemolysin subunit a | protein | 270 | 4% helix, 62% strand | B1Q017 |
| D | Gamma-hemolysin subunit a | protein | 255 | 4% helix, 65% strand | B1Q017 |
Ligands and binding sites
- PQJ · fos-choline-14 · ligand · 3 copies · chains A
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, D
- ACT · Acetate ion · additive · 8 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.72 | 0.78 | 86 | SO4, ACT |
| 2 | 189 | 0.51 | 0.77 | 33 | SO4 |
| 3 | 231 | 0.49 | 0.75 | 29 | ACT |
| 4 | 191 | 0.47 | 0.76 | 25 | ACT |
| 5 | 139 | 0.42 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2781 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6U3Y · Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S.… · 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 Q5FBD2
- Every structure of UniProt B1Q017
- Elsewhere: RCSB PDB 6U3Y · PDBe 6U3Y · UniProt Q5FBD2 · UniProt B1Q017
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