Research workbench
Complex of fmdv and M8 nab
Analyse Complex of fmdv and M8 nab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DSS
- Type
- protein
- Length
- 797 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M8 nab; VP1 of O type fmdv capsid; VP2 of O-type fmdv capsid; VP3 of O-type fmdv capsid…
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M8 nab | protein | 126 | 2% helix, 42% strand | — |
| 1 | VP1 of O type fmdv capsid | protein | 200 | 19% helix, 27% strand | — |
| 2 | VP2 of O-type fmdv capsid | protein | 206 | 9% helix, 43% strand | — |
| 3 | VP3 of O-type fmdv capsid | protein | 219 | 6% helix, 33% strand | — |
| 4 | VP4 of O-type fmdv capsid | protein | 46 | 24% helix, 2% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.81 | 0.82 | 101 | empty |
| 2 | 1107 | 0.73 | 0.76 | 83 | empty |
| 3 | 63 | 0.68 | 0.95 | 27 | empty |
| 4 | 127 | 0.49 | 0.80 | 28 | empty |
| 5 | 131 | 0.46 | 0.78 | 17 | empty |
Interfaces
8 interfaces between chains.
- 1–2 · 1405 Ų buried · 13 hydrogen bonds · protein-protein
- 1–3 · 989 Ų buried · 8 hydrogen bonds · protein-protein
- A–1 · 877 Ų buried · 11 hydrogen bonds · protein-protein
- 2–3 · 851 Ų buried · 8 hydrogen bonds · protein-protein
- 1–4 · 826 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DSS · Complex of FMDV and M8 Nab · the same entry in another collection · chain A against A, 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 7DSS · PDBe 7DSS
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