Research workbench
Foot and mouth disease virus O/TIBET/99-bound the single chain fragmen antibody R50
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
- 7D3M
- Type
- protein
- Length
- 907 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; R50 vh; R50 vl
- Pockets
- 9 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 6% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | O/TIBET/99 VP1 | protein | 183 | 4% helix, 21% strand | — |
| 2 | O/TIBET/99 VP2 | protein | 206 | 5% helix, 35% strand | — |
| 3 | O/TIBET/99 VP3 | protein | 219 | 7% helix, 26% strand | — |
| 4 | O/TIBET/99 VP4 | protein | 46 | 9% helix, 2% strand | — |
| H | R50 vh | protein | 145 | 6% helix, 19% strand | — |
| L | R50 vl | protein | 108 | 3% helix, 28% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.74 | 0.85 | 46 | empty |
| 2 | 528 | 0.69 | 0.79 | 48 | empty |
| 3 | 413 | 0.67 | 0.79 | 35 | empty |
| 4 | 258 | 0.64 | 0.82 | 35 | empty |
| 5 | 186 | 0.53 | 0.79 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1474 Ų buried · 12 hydrogen bonds · protein-protein
- 1–2 · 1321 Ų buried · 13 hydrogen bonds · protein-protein
- 1–3 · 1024 Ų buried · 12 hydrogen bonds · protein-protein
- 2–3 · 929 Ų buried · 8 hydrogen bonds · protein-protein
- 1–H · 869 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7D3M · Foot and mouth disease virus O/TIBET/99-bound the single chain fragmen antibody R50 · 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 7D3M · PDBe 7D3M
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