Research workbench
The structure of coxsackievirus A16 mature virion in complex with Fab 8C4
Analyse The structure of coxsackievirus A16 mature virion in complex with Fab 8C4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y7M
- Type
- protein
- Length
- 1,259 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 light…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- M4TAU2, A9LXZ4, A8TSC7
- Ligands
- SPH
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 8% helix, 36% 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 | 287 | 8% helix, 27% 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 | 12% helix, 33% strand | A9LXZ4 |
| D | Capsid protein VP4 | protein | 58 | 12% helix, 12% strand | A8TSC7 |
| G | The light chain of Fab 8C4 | protein | 213 | 3% helix, 47% strand | — |
| F | The heavy chain of Fab 8C4 | protein | 214 | 4% helix, 45% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.81 | 0.91 | 61 | SPH |
| 2 | 383 | 0.66 | 0.80 | 49 | empty |
| 3 | 101 | 0.62 | 0.88 | 24 | empty |
| 4 | 143 | 0.48 | 0.78 | 29 | empty |
| 5 | 175 | 0.46 | 0.75 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4014 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2432 Ų buried · 35 hydrogen bonds · protein-protein
- G–F · 1738 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1682 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1546 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7Y7M · The structure of coxsackievirus A16 mature virion in complex with Fab 8C4 · 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 7Y7M · PDBe 7Y7M · UniProt M4TAU2 · UniProt A9LXZ4 · UniProt A8TSC7
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