MolNFT v1 · #101369 · protein
Clostridium difficile toxin B crop domain in complex with Fab domains of neutralizing antibody bezlotoxumab
4NP4: “Clostridium difficile toxin B crop domain in complex with Fab domains of neutralizing antibody bezlotoxumab”. X-ray diffraction, 14 pockets (best druggability 0.66). MolNFT v1 #101369 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4NP4
- Type
- protein
- Length
- 1,133 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; Bezlotoxumab heavy chain; Bezlotoxumab light chain
- UniProt
- P18177
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B | protein | 271 | 0% helix, 52% strand | P18177 |
| H | Bezlotoxumab heavy chain | protein | 215 | 6% helix, 52% strand | — |
| I | Bezlotoxumab heavy chain | protein | 221 | 5% helix, 50% strand | — |
| L, M | Bezlotoxumab light chain | protein | 213 | 6% helix, 54% strand | — |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.66 | 0.75 | 61 | empty |
| 2 | 67 | 0.55 | 0.88 | 24 | empty |
| 3 | 384 | 0.54 | 0.73 | 48 | empty |
| 4 | 218 | 0.46 | 0.74 | 32 | empty |
| 5 | 189 | 0.44 | 0.74 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1815 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 1740 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 717 Ų buried · 19 hydrogen bonds · protein-protein
- A–I · 708 Ų buried · 16 hydrogen bonds · protein-protein
- A–M · 258 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4NP4 · Clostridium difficile toxin B CROP domain in complex with FAB domains of neutralizing… · 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 P18177
- Elsewhere: RCSB PDB 4NP4 · PDBe 4NP4 · UniProt P18177
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