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Density-fitted model structure of antibody variable domains of TYTX4 in complex with pltb pentamer of typhoid toxin
Analyse Density-fitted model structure of antibody variable domains of TYTX4 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K7I
- Type
- protein
- Length
- 1,705 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pertussis-like toxin subunit; Fab light chain variable domain; Fab heavy chain…
- UniProt
- Q8Z6A3
- Pockets
- 12 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 5% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Putative pertussis-like toxin subunit | protein | 114 | 15% helix, 38% strand | Q8Z6A3 |
| L, K, N, Q, Y | Fab light chain variable domain | protein | 108 | 0% helix, 40% strand | — |
| H, J, M, P, X | Fab heavy chain variable domain | protein | 119 | 0% helix, 21% strand | — |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.69 | 0.75 | 67 | empty |
| 2 | 824 | 0.69 | 0.75 | 55 | empty |
| 3 | 763 | 0.67 | 0.75 | 53 | empty |
| 4 | 747 | 0.66 | 0.74 | 61 | empty |
| 5 | 684 | 0.65 | 0.75 | 56 | empty |
Interfaces
30 interfaces between chains.
- A–B · 1117 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1109 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1087 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 1083 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1055 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 7K7I · Density-fitted Model Structure of Antibody Variable Domains of TyTx4 in Complex with PltB… · the same entry in another collection · chain P against P, 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 Q8Z6A3
- Elsewhere: RCSB PDB 7K7I · PDBe 7K7I · UniProt Q8Z6A3
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