Research workbench
The cryo-EM structure of coxsackievirus A16 empty particle
Analyse The cryo-EM structure of coxsackievirus A16 empty particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LHC
- Type
- protein
- Length
- 636 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 0.62
Structure
electron microscopy · 3 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 209 | 4% helix, 32% strand | A0A2S1BJ89 |
| B | VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 208 | 11% helix, 37% strand | A0A1D3TZV2 |
| C | VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 219 | 11% helix, 26% 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 | 286 | 0.62 | 0.80 | 39 | empty |
| 2 | 93 | 0.56 | 0.85 | 23 | empty |
| 3 | 141 | 0.53 | 0.80 | 21 | empty |
| 4 | 130 | 0.44 | 0.76 | 24 | empty |
| 5 | 122 | 0.44 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2786 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1560 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1455 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6LHC · The cryo-EM structure of coxsackievirus A16 empty particle · 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
- Elsewhere: RCSB PDB 6LHC · PDBe 6LHC · UniProt A0A2S1BJ89 · UniProt A0A1D3TZV2 · UniProt A0A2R4NBT3
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