Research workbench
Structure of the complex of a Fab fragment of a neutralizing antibody with foot and mouth disease virus
Analyse Structure of the complex of a Fab fragment of a neutralizing antibody with foot… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QGC
- Type
- protein
- Length
- 1,082 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (virus capsid protein VP1); Protein (virus capsid protein VP2); Protein (virus…
- UniProt
- Q9QCE2, P15072
- Pockets
- 11 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Protein (virus capsid protein VP1) | protein | 183 | 16% helix, 33% strand | Q9QCE2 |
| 2 | Protein (virus capsid protein VP2) | protein | 218 | 8% helix, 41% strand | Q9QCE2 |
| 3 | Protein (virus capsid protein VP3) | protein | 219 | 8% helix, 30% strand | P15072 |
| 4 | Protein (immunoglobulin light chain) | protein | 218 | 7% helix, 52% strand | — |
| A | Protein (immunoglobulin heavy chain) | protein | 220 | 10% helix, 49% strand | — |
| 5 | Protein (gh-loop from virus capsid protein VP1) | protein | 24 | 13% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.81 | 0.83 | 92 | empty |
| 2 | 53 | 0.70 | 0.97 | 20 | empty |
| 3 | 277 | 0.61 | 0.79 | 35 | empty |
| 4 | 375 | 0.57 | 0.75 | 45 | empty |
| 5 | 119 | 0.47 | 0.79 | 23 | empty |
Interfaces
11 interfaces between chains.
- 4–A · 1822 Ų buried · 15 hydrogen bonds · protein-protein
- 1–2 · 1268 Ų buried · 24 hydrogen bonds · protein-protein
- 1–3 · 1101 Ų buried · 18 hydrogen bonds · protein-protein
- 2–3 · 883 Ų buried · 13 hydrogen bonds · protein-protein
- A–5 · 374 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 1QGC · Structure of the complex of a Fab fragment of a neutralizing antibody with foot and mouth… · the same entry in another collection · chain 1 against 1, 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 Q9QCE2
- Every structure of UniProt P15072
- Elsewhere: RCSB PDB 1QGC · PDBe 1QGC · UniProt Q9QCE2 · UniProt P15072
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