Research workbench
Cryo-EM structure of mature coxsackievirus A10 at pH 5.5
Analyse Cryo-EM structure of mature coxsackievirus A10 at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BZO
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- UniProt
- G0YPI2
- Ligands
- SPH
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 271 | 8% helix, 28% strand | — |
| B | Capsid protein VP2 | protein | 246 | 11% helix, 28% strand | G0YPI2 |
| C | Capsid protein VP3 | protein | 239 | 8% helix, 30% strand | G0YPI2 |
| D | Capsid protein VP4 | protein | 37 | 16% helix, 8% strand | G0YPI2 |
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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.81 | 0.90 | 44 | SPH |
| 2 | 267 | 0.58 | 0.79 | 40 | empty |
| 3 | 81 | 0.45 | 0.81 | 12 | empty |
| 4 | 106 | 0.45 | 0.78 | 16 | empty |
| 5 | 68 | 0.40 | 0.80 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3809 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2291 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1696 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1088 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 773 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7BZO · Cryo-EM structure of mature Coxsackievirus A10 at pH 5.5 · 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 G0YPI2
- Elsewhere: RCSB PDB 7BZO · PDBe 7BZO · UniProt G0YPI2
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