Research workbench
Coxsackievirus B3 at PH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10MIN
Analyse Coxsackievirus B3 at PH7.4 (VP3-234Q) incubation with coxsackievirus and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VYK
- Type
- protein
- Length
- 920 residues
- Chains
- 5
- 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
- P03313, P78310
- Ligands
- PLM
- Pockets
- 14 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 267 | 9% helix, 31% strand | P03313 |
| B | Capsid protein VP2 | protein | 255 | 6% helix, 35% strand | P03313 |
| C | Capsid protein VP3 | protein | 237 | 8% helix, 30% strand | P03313 |
| D | Capsid protein VP4 | protein | 57 | 0% helix, 16% strand | P03313 |
| E | Coxsackievirus and adenovirus receptor | protein | 104 | 0% helix, 44% strand | P78310 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.77 | 0.83 | 78 | PLM |
| 2 | 522 | 0.72 | 0.81 | 54 | empty |
| 3 | 157 | 0.50 | 0.78 | 20 | empty |
| 4 | 115 | 0.48 | 0.79 | 24 | empty |
| 5 | 79 | 0.48 | 0.83 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–C · 4217 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2135 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1573 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1179 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 900 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7VYK · Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus… · the same entry in another collection · chain A against A, TM-score 1.00
- P78310 · AlphaFold monomer V2.0 prediction for coxsackievirus and adenovirus receptor (P78310) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 P03313
- Every structure of UniProt P78310
- Elsewhere: RCSB PDB 7VYK · PDBe 7VYK · UniProt P03313 · UniProt P78310
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