MolNFT v1 · #179502 · protein
Density-fitted model structure of antibody variable domains of TYTX1 in complex with pltb pentamer of typhoid toxin
7K7H · Pertussis like toxin subunit B: “Density-fitted model structure of antibody variable domains of TYTX1 in complex with pltb pentamer of typhoid…”. Electron microscopy, 4 pockets (best druggability 0.69). MolNFT v1 #179502 on…
- PDB
- 7K7H
- Type
- protein
- Length
- 816 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis like toxin subunit B; Fab light chain variable domain; Fab heavy chain variable…
- UniProt
- A0A286LNT9, A0A4Z0MXD9
- Pockets
- 4 · best druggability 0.69
Structure
electron microscopy · 4 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Pertussis like toxin subunit B | protein | 114 | 18% helix, 39% strand | A0A286LNT9 |
| L | Fab light chain variable domain | protein | 114 | 0% helix, 31% strand | — |
| H | Fab heavy chain variable domain | protein | 118 | 3% helix, 47% strand | — |
| G | Pertussis toxin-like subunit arta | protein | 14 | 64% helix, 0% strand | A0A4Z0MXD9 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.69 | 0.86 | 28 | empty |
| 2 | 334 | 0.66 | 0.81 | 41 | empty |
| 3 | 322 | 0.57 | 0.77 | 31 | empty |
| 4 | 51 | 0.32 | 0.78 | 12 | empty |
Interfaces
14 interfaces between chains.
- B–E · 1117 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1080 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1078 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1015 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7K7H · Density-fitted Model Structure of Antibody Variable Domains of TyTx1 in Complex with PltB… · the same entry in another collection · chain E against E, 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 A0A286LNT9
- Every structure of UniProt A0A4Z0MXD9
- Elsewhere: RCSB PDB 7K7H · PDBe 7K7H · UniProt A0A286LNT9 · UniProt A0A4Z0MXD9
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