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The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab NA9D7
Analyse The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LHQ
- Type
- protein
- Length
- 1,055 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.06
- Source
- Coxsackievirus A16; Mus musculus
- Molecule
- VP1 protein; VP2 protein; VP3 protein; VP4 protein; light chain variable region of Fab…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A2S1BJ89, A0A1D3TZV2, A0A2R4NBT3, A5HX42
- Ligands
- SPH
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · resolution 3.06 · 6 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 protein | protein | 283 | 10% helix, 29% strand | A0A2S1BJ89 |
| B | VP2 protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 245 | 9% helix, 36% strand | A0A1D3TZV2 |
| C | VP3 protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 10% helix, 30% strand | A0A2R4NBT3 |
| D | VP4 protein | protein | 57 | 12% helix, 9% strand | A5HX42 |
| L | light chain variable region of Fab NA9D7 | protein | 108 | 3% helix, 44% strand | — |
| H | heavy chain variable region of Fab NA9D7 | protein | 120 | 3% helix, 47% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.84 | 0.85 | 130 | SPH |
| 2 | 286 | 0.68 | 0.83 | 51 | empty |
| 3 | 155 | 0.62 | 0.85 | 33 | empty |
| 4 | 70 | 0.58 | 0.88 | 22 | empty |
| 5 | 56 | 0.56 | 0.89 | 21 | empty |
Interfaces
11 interfaces between chains.
- A–C · 3892 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2415 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1659 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1442 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6LHQ · The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab NA9D7 · 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 A0A2S1BJ89
- Every structure of UniProt A0A1D3TZV2
- Every structure of UniProt A0A2R4NBT3
- Every structure of UniProt A5HX42
- Elsewhere: RCSB PDB 6LHQ · PDBe 6LHQ · UniProt A0A2S1BJ89 · UniProt A0A1D3TZV2 · UniProt A0A2R4NBT3 · UniProt A5HX42
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