MolNFT v1 · #155746 · protein
The cryo-EM structure of coxsackievirus A16 mature virion
6LHA · VP1 protein: “The cryo-EM structure of coxsackievirus A16 mature virion”. Electron microscopy, 1 ligand (SPH), 16 pockets (best druggability 0.83). MolNFT v1 #155746 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LHA
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 protein; VP2 protein; VP3 protein; VP4 protein
- 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
- 16 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 9% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 protein | protein | 283 | 8% 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 | 8% helix, 35% strand | A0A1D3TZV2 |
| C | VP3 protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 12% helix, 28% strand | A0A2R4NBT3 |
| D | VP4 protein | protein | 57 | 12% helix, 9% strand | A5HX42 |
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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.83 | 0.89 | 59 | SPH |
| 2 | 59 | 0.61 | 0.92 | 21 | empty |
| 3 | 114 | 0.57 | 0.85 | 23 | empty |
| 4 | 255 | 0.56 | 0.78 | 29 | empty |
| 5 | 144 | 0.46 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3993 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2416 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1675 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1463 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1097 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6LHA · The cryo-EM structure of coxsackievirus A16 mature virion · 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 6LHA · PDBe 6LHA · UniProt A0A2S1BJ89 · UniProt A0A1D3TZV2 · UniProt A0A2R4NBT3 · UniProt A5HX42
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