Research workbench
The cryo-EM structure of coxsackievirus A16 a-particle
Analyse The cryo-EM structure of coxsackievirus A16 a-particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LHB
- Type
- protein
- Length
- 648 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A2S1BJ89, A0A1D3TZV2, A0A2R4NBT3
- Pockets
- 10 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 212 | 7% helix, 30% strand | A0A2S1BJ89 |
| B | VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 210 | 11% helix, 36% strand | A0A1D3TZV2 |
| C | VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 226 | 11% helix, 35% strand | A0A2R4NBT3 |
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 | 279 | 0.61 | 0.79 | 49 | empty |
| 2 | 139 | 0.51 | 0.79 | 21 | empty |
| 3 | 171 | 0.50 | 0.77 | 23 | empty |
| 4 | 170 | 0.46 | 0.76 | 18 | empty |
| 5 | 150 | 0.45 | 0.76 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3316 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1555 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1355 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6LHB · The cryo-EM structure of coxsackievirus A16 A-particle · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 6LHB · PDBe 6LHB · UniProt A0A2S1BJ89 · UniProt A0A1D3TZV2 · UniProt A0A2R4NBT3
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