Research workbench
Foot and mouth disease virus O/TIBET/99-bound the single chain fragmen antibody B77
Analyse Foot and mouth disease virus O/TIBET/99-bound the single chain fragmen antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3K
- Type
- protein
- Length
- 846 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O/TIBET/99 VP1; O/TIBET/99 VP2; O/TIBET/99 VP3; O/TIBET/99 VP4; B77 vh; B77 vl
- Pockets
- 14 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 6% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | O/TIBET/99 VP1 | protein | 183 | 6% helix, 20% strand | — |
| 2 | O/TIBET/99 VP2 | protein | 206 | 3% helix, 27% strand | — |
| 3 | O/TIBET/99 VP3 | protein | 219 | 6% helix, 26% strand | — |
| 4 | O/TIBET/99 VP4 | protein | 44 | 18% helix, 2% strand | — |
| H | B77 vh | protein | 109 | 3% helix, 20% strand | — |
| L | B77 vl | protein | 85 | 6% helix, 6% strand | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.74 | 0.79 | 63 | empty |
| 2 | 129 | 0.72 | 0.92 | 29 | empty |
| 3 | 353 | 0.68 | 0.81 | 36 | empty |
| 4 | 422 | 0.64 | 0.77 | 53 | empty |
| 5 | 316 | 0.58 | 0.76 | 41 | empty |
Interfaces
9 interfaces between chains.
- 1–2 · 1190 Ų buried · 15 hydrogen bonds · protein-protein
- 1–3 · 1052 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 958 Ų buried · 6 hydrogen bonds · protein-protein
- 2–3 · 949 Ų buried · 10 hydrogen bonds · protein-protein
- 1–4 · 833 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7D3K · Foot and mouth disease virus O/TIBET/99-bound the single chain fragmen antibody B77 · 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
- Elsewhere: RCSB PDB 7D3K · PDBe 7D3K
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