MolNFT v1 · #14257 · protein
Perfringolysin O, new crystal form
1M3I: “Perfringolysin O, new crystal form”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #14257 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1M3I
- Type
- protein
- Length
- 1,860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Perfringolysin O
- UniProt
- P19995
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Perfringolysin O | protein | 465 | 21% helix, 40% strand | P19995 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.78 | 0.83 | 72 | empty |
| 2 | 1124 | 0.77 | 0.79 | 111 | empty |
| 3 | 844 | 0.77 | 0.81 | 83 | empty |
| 4 | 674 | 0.74 | 0.80 | 59 | empty |
| 5 | 326 | 0.68 | 0.83 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1647 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1542 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 310 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1M3I · Perfringolysin O, new crystal form · 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 P19995
- Elsewhere: RCSB PDB 1M3I · PDBe 1M3I · UniProt P19995
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