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
- 6U49
- Type
- protein
- Length
- 2,051 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hemolysin
- UniProt
- P09616
- Ligands
- PQJ, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Alpha-hemolysin | protein | 293 | 4% helix, 58% strand | P09616 |
Ligands and binding sites
- PQJ · fos-choline-14 · ligand · 21 copies · chains A, F, C, G, B, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.80 | 0.81 | 99 | PQJ, SO4 |
| 2 | 278 | 0.72 | 0.86 | 33 | empty |
| 3 | 255 | 0.72 | 0.86 | 32 | empty |
| 4 | 267 | 0.71 | 0.86 | 33 | empty |
| 5 | 441 | 0.71 | 0.81 | 51 | PQJ |
Interfaces
14 interfaces between chains.
- A–B · 3016 Ų buried · 66 hydrogen bonds · protein-protein
- A–G · 3011 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3008 Ų buried · 67 hydrogen bonds · protein-protein
- F–G · 3005 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 2993 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 6U49 · Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S.… · the same entry in another collection · chain G against G, TM-score 1.00
- P09616 · AlphaFold monomer V2.0 prediction for alpha-hemolysin (P09616) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P09616
- Elsewhere: RCSB PDB 6U49 · PDBe 6U49 · UniProt P09616
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