MolNFT v1 · #100924 · protein
Crystal structure of clostridium difficile toxin a fragment tcda-A1 bound to A20.1 vhh
4NBX: “Crystal structure of clostridium difficile toxin a fragment tcda-A1 bound to A20.1 vhh”. X-ray diffraction, 2 pockets (best druggability 0.49). MolNFT v1 #100924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NBX
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tcda; A20.1 vhh
- UniProt
- I6YE93
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tcda | protein | 143 | 0% helix, 49% strand | I6YE93 |
| B | A20.1 vhh | protein | 123 | 5% helix, 51% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.49 | 0.85 | 18 | empty |
| 2 | 113 | 0.45 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4NBX · Crystal Structure of Clostridium difficile Toxin A fragment TcdA-A1 Bound to A20.1 VHH · 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 I6YE93
- Elsewhere: RCSB PDB 4NBX · PDBe 4NBX · UniProt I6YE93
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