MolNFT v1 · #188138 · protein
Cryoem structure of sfab cop-3 complex with human claudin-4 and clostridium perfringens enterotoxin C-terminal domain
7TDN: “Cryoem structure of sfab cop-3 complex with human claudin-4 and clostridium perfringens enterotoxin…”. Electron microscopy, 11 pockets (best druggability 0.85). MolNFT v1 #188138 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7TDN
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Claudin-4; Heat-labile enterotoxin B chain; Cop-3 Fab heavy chain; Cop-3 Fab light chain
- UniProt
- O14493, P01558
- Pockets
- 11 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Claudin-4 | protein | 182 | 57% helix, 12% strand | O14493 |
| B | Heat-labile enterotoxin B chain | protein | 123 | 5% helix, 46% strand | P01558 |
| H | Cop-3 Fab heavy chain | protein | 226 | 5% helix, 44% strand | — |
| L | Cop-3 Fab light chain | protein | 215 | 6% helix, 41% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.85 | 0.93 | 60 | empty |
| 2 | 851 | 0.82 | 0.84 | 83 | empty |
| 3 | 89 | 0.77 | 0.97 | 21 | empty |
| 4 | 79 | 0.76 | 0.98 | 22 | empty |
| 5 | 134 | 0.58 | 0.84 | 26 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1735 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 833 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 8 hydrogen bonds · protein-protein
- B–L · 188 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7TDN · CryoEM Structure of sFab COP-3 Complex with human claudin-4 and Clostridium perfringens… · 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 0.90
- O14493 · AlphaFold monomer V2.0 prediction for claudin-4 (O14493) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 O14493
- Every structure of UniProt P01558
- Elsewhere: RCSB PDB 7TDN · PDBe 7TDN · UniProt O14493 · UniProt P01558
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