MolNFT v1 · #102975 · protein
Complex of shiga toxin 2E with a neutralizing single-domain antibody
4P2C · Shiga toxin 2E, subunit a: “Complex of shiga toxin 2E with a neutralizing single-domain antibody”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #102975 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4P2C
- Type
- protein
- Length
- 1,228 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga toxin 2E, subunit a; Shiga toxin 2E, subunit B; Nanobody 1, anti-F4+ETEC bacteria…
- UniProt
- Q7WUF4, Q47644, R9VYW2
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shiga toxin 2E, subunit a | protein | 280 | 34% helix, 22% strand | Q7WUF4 |
| B, C, D, E, F | Shiga toxin 2E, subunit B | protein | 68 | 15% helix, 40% strand | Q47644 |
| G | Nanobody 1, anti-F4+ETEC bacteria vhh variable region | protein | 121 | 8% helix, 49% strand | R9VYW2 |
| H, I, K | Nanobody 1, anti-F4+ETEC bacteria vhh variable region | protein | 120 | 8% helix, 49% strand | R9VYW2 |
| J | Nanobody 1, anti-F4+ETEC bacteria vhh variable region | protein | 127 | 8% helix, 46% strand | R9VYW2 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.71 | 0.77 | 68 | empty |
| 2 | 751 | 0.68 | 0.76 | 87 | empty |
| 3 | 343 | 0.57 | 0.76 | 47 | empty |
| 4 | 322 | 0.56 | 0.76 | 36 | empty |
| 5 | 288 | 0.54 | 0.76 | 36 | empty |
Interfaces
30 interfaces between chains.
- B–F · 730 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 725 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 720 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 713 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4P2C · Complex of Shiga toxin 2e with a neutralizing single-domain antibody · 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 Q7WUF4
- Every structure of UniProt Q47644
- Every structure of UniProt R9VYW2
- Elsewhere: RCSB PDB 4P2C · PDBe 4P2C · UniProt Q7WUF4 · UniProt Q47644 · UniProt R9VYW2
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