MolNFT v1 · #167842 · protein
Density-fitted model structure of antibody variable domains of TYTX11 in complex with typhoid toxin
6VX4 · Variable domain of kappa chain of TYTX11 antibody: “Density-fitted model structure of antibody variable domains of TYTX11 in complex with typhoid toxin”. Electron microscopy, 11 pockets (best druggability 0.69). MolNFT v1 #167842 on…
- PDB
- 6VX4
- Type
- protein
- Length
- 1,265 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable domain of kappa chain of TYTX11 antibody; Pertussis like toxin subunit B…
- EC
- 3.1.-.-
- UniProt
- A0A286LNT9, A0A3Z7CEY9, A0A447PE99
- Pockets
- 11 · best druggability 0.69
Structure
electron microscopy · 5 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Variable domain of kappa chain of TYTX11 antibody | protein | 106 | 0% helix, 42% strand | — |
| C, A, B, D, E | Pertussis like toxin subunit B | protein | 114 | 16% helix, 41% strand | A0A286LNT9 |
| H | Variable domain of heavy chain of antibody TYTX11 | protein | 118 | 8% helix, 52% strand | — |
| G | Pertussis toxin-like subunit arta | protein | 224 | 26% helix, 21% strand | A0A3Z7CEY9 |
| F | Cytolethal distending toxin subunit B (EC 3.1.-.-) | protein | 247 | 13% helix, 28% strand | A0A447PE99 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.69 | 0.96 | 16 | empty |
| 2 | 427 | 0.67 | 0.80 | 60 | empty |
| 3 | 565 | 0.66 | 0.77 | 64 | empty |
| 4 | 125 | 0.58 | 0.84 | 22 | empty |
| 5 | 157 | 0.51 | 0.79 | 30 | empty |
Interfaces
15 interfaces between chains.
- G–F · 1232 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1105 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1105 Ų buried · 28 hydrogen bonds · protein-protein
- C–A · 1098 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6VX4 · Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with… · the same entry in another collection · chain K against K, 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 A0A3Z7CEY9
- Every structure of UniProt A0A447PE99
- Elsewhere: RCSB PDB 6VX4 · PDBe 6VX4 · UniProt A0A286LNT9 · UniProt A0A3Z7CEY9 · UniProt A0A447PE99
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