Research workbench
Crystal structure of the M113F alpha-hemolysin mutant complexed with beta-cyclodextrin
Analyse Crystal structure of the M113F alpha-hemolysin mutant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M3R
- 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 0.75
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Alpha-hemolysin | protein | 293 | 3% helix, 58% strand | P09616 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains C, D, E, F, G, A, B
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 | 639 | 0.75 | 0.81 | 72 | empty |
| 2 | 366 | 0.73 | 0.84 | 62 | empty |
| 3 | 525 | 0.73 | 0.81 | 64 | empty |
| 4 | 394 | 0.72 | 0.83 | 51 | empty |
| 5 | 635 | 0.71 | 0.79 | 60 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2993 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 2982 Ų buried · 64 hydrogen bonds · protein-protein
- A–G · 2978 Ų buried · 61 hydrogen bonds · protein-protein
- F–G · 2944 Ų buried · 67 hydrogen bonds · protein-protein
- E–F · 2938 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 3M3R · Crystal structure of the M113F alpha-hemolysin mutant complexed with 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 3M3R · PDBe 3M3R · UniProt P09616
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