Research workbench
Fmdv capsid in complex with M170 nab
Analyse Fmdv capsid in complex with M170 nab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DST
- Type
- protein
- Length
- 772 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 of O type fmdv capsid; VP2 of O type fmdv capsid; VP3 of O type fmdv capsid; VP4 of O…
- Pockets
- 8 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 of O type fmdv capsid | protein | 184 | 15% helix, 30% strand | — |
| B | VP2 of O type fmdv capsid | protein | 206 | 8% helix, 45% strand | — |
| C | VP3 of O type fmdv capsid | protein | 219 | 8% helix, 33% strand | — |
| D | VP4 of O type fmdv capsid | protein | 46 | 22% helix, 0% strand | — |
| E | M170 nab | protein | 117 | 5% helix, 53% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.76 | 0.79 | 114 | empty |
| 2 | 543 | 0.68 | 0.78 | 52 | empty |
| 3 | 407 | 0.67 | 0.80 | 39 | empty |
| 4 | 214 | 0.63 | 0.82 | 28 | empty |
| 5 | 148 | 0.46 | 0.77 | 23 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1314 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 790 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 739 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DST · FMDV capsid in complex with M170 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 7DST · PDBe 7DST
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