Research workbench
Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin
Analyse Crystal structure of the M113N mutant of alpha-hemolysin bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M4E
- 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
- GLC
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Alpha-hemolysin | protein | 293 | 5% helix, 58% strand | P09616 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 7 copies · chains C, D, A, B, G, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.74 | 0.85 | 62 | empty |
| 2 | 440 | 0.74 | 0.83 | 58 | empty |
| 3 | 512 | 0.73 | 0.81 | 57 | empty |
| 4 | 642 | 0.72 | 0.79 | 66 | empty |
| 5 | 289 | 0.71 | 0.85 | 35 | empty |
Interfaces
14 interfaces between chains.
- A–G · 2971 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 2956 Ų buried · 60 hydrogen bonds · protein-protein
- F–G · 2942 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 2926 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 2911 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 3M4E · Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin · 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 3M4E · PDBe 3M4E · UniProt P09616
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