MolNFT v1 · #142936 · protein
Crystal structure of mouse claudin-3 in complex with C-terminal fragment of clostridium perfringens enterotoxin
6AKE: “Crystal structure of mouse claudin-3 in complex with C-terminal fragment of clostridium perfringens…”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #142936 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6AKE
- Type
- protein
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Claudin-3; Heat-labile enterotoxin B chain
- UniProt
- Q9Z0G9, P01558
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Claudin-3 | protein | 179 | 65% helix, 12% strand | Q9Z0G9 |
| B | Heat-labile enterotoxin B chain | protein | 117 | 9% helix, 54% strand | P01558 |
| C | Claudin-3 | protein | 168 | 66% helix, 11% strand | Q9Z0G9 |
| D | Heat-labile enterotoxin B chain | protein | 115 | 4% helix, 46% strand | P01558 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.69 | 0.78 | 69 | empty |
| 2 | 389 | 0.58 | 0.75 | 46 | empty |
| 3 | 321 | 0.58 | 0.77 | 46 | empty |
| 4 | 106 | 0.41 | 0.76 | 15 | empty |
| 5 | 56 | 0.34 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1080 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 1048 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 992 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6AKE · Crystal structure of mouse claudin-3 in complex with C-terminal fragment of Clostridium… · the same entry in another collection · chain A against A, TM-score 1.00
- P01558 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P01558) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9Z0G9 · AlphaFold monomer V2.0 prediction for claudin-3 (Q9Z0G9) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q9Z0G9
- Every structure of UniProt P01558
- Elsewhere: RCSB PDB 6AKE · PDBe 6AKE · UniProt Q9Z0G9 · UniProt P01558
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