MolNFT v1 · #175854 · protein
Foot and mouth disease virus A/WH/CHA/09-bound the single chain fragme antibody R50
7D3R · A/WH/CHA/09 VP1: “Foot and mouth disease virus A/WH/CHA/09-bound the single chain fragme antibody R50”. Electron microscopy, 8 pockets (best druggability 0.80). MolNFT v1 #175854 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7D3R
- Type
- protein
- Length
- 909 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A/WH/CHA/09 VP1; A/WH/CHA/09 VP2; A/WH/CHA/09 VP3; A/WH/CHA/09 VP4; R50 vh; R50 vl
- Pockets
- 8 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | A/WH/CHA/09 VP1 | protein | 186 | 11% helix, 27% strand | — |
| 2 | A/WH/CHA/09 VP2 | protein | 206 | 6% helix, 41% strand | — |
| 3 | A/WH/CHA/09 VP3 | protein | 220 | 7% helix, 31% strand | — |
| 4 | A/WH/CHA/09 VP4 | protein | 45 | 27% helix, 2% strand | — |
| H | R50 vh | protein | 144 | 6% helix, 22% strand | — |
| L | R50 vl | protein | 108 | 3% helix, 40% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.80 | 0.91 | 59 | empty |
| 2 | 370 | 0.58 | 0.76 | 47 | empty |
| 3 | 52 | 0.44 | 0.83 | 17 | empty |
| 4 | 112 | 0.43 | 0.77 | 23 | empty |
| 5 | 162 | 0.41 | 0.73 | 24 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1494 Ų buried · 18 hydrogen bonds · protein-protein
- 1–2 · 1424 Ų buried · 20 hydrogen bonds · protein-protein
- 3–4 · 1220 Ų buried · 14 hydrogen bonds · protein-protein
- 1–3 · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- 2–3 · 830 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7D3R · Foot and mouth disease virus A/WH/CHA/09-bound the single chain fragme antibody R50 · the same entry in another collection · chain H against H, 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 7D3R · PDBe 7D3R
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