Research workbench
Cryo-EM structure of coxsackievirus A16 in complex with a neutralizing antibody 9B5
Analyse Cryo-EM structure of coxsackievirus A16 in complex with a neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YMS
- Type
- protein
- Length
- 1,258 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; The heavy…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- M4TAU2, A9LXZ4, A8TSC7
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 282 | 9% helix, 28% strand | M4TAU2 |
| B | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 245 | 10% helix, 37% strand | A9LXZ4 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 11% helix, 33% strand | A9LXZ4 |
| D | Capsid protein VP4 | protein | 58 | 7% helix, 5% strand | A8TSC7 |
| F | The heavy chain of Fab 9B5 | protein | 218 | 3% helix, 41% strand | — |
| E | The light chain of Fab 9B5 | protein | 213 | 0% helix, 35% strand | — |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.81 | 0.90 | 55 | empty |
| 2 | 380 | 0.59 | 0.76 | 44 | empty |
| 3 | 216 | 0.56 | 0.79 | 27 | empty |
| 4 | 123 | 0.54 | 0.82 | 22 | empty |
| 5 | 68 | 0.53 | 0.87 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3970 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2275 Ų buried · 39 hydrogen bonds · protein-protein
- F–E · 1952 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1667 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1473 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7YMS · Cryo-EM structure of Coxsackievirus A16 in complex with a neutralizing antibody 9B5 · 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
- Every structure of UniProt M4TAU2
- Every structure of UniProt A9LXZ4
- Every structure of UniProt A8TSC7
- Elsewhere: RCSB PDB 7YMS · PDBe 7YMS · UniProt M4TAU2 · UniProt A9LXZ4 · UniProt A8TSC7
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