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Coxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievirus and adenovirus receptor for 10min
Analyse Coxsackievirus B3 at pH7.4 (VP3-234E) 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
- 7VYM
- Type
- protein
- Length
- 921 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.68
- Source
- Coxsackievirus B3; Homo sapiens
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4…
- UniProt
- P78310
- Pockets
- 12 · best druggability 0.73
Structure
electron microscopy · resolution 3.68 · 5 distinct chains · 9% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 267 | 11% helix, 30% strand | — |
| B | Capsid protein VP2 | protein | 255 | 8% helix, 35% strand | — |
| C | Capsid protein VP3 | protein | 237 | 13% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 57 | 5% helix, 16% strand | — |
| E | Coxsackievirus and adenovirus receptor | protein | 105 | 0% helix, 41% strand | P78310 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.73 | 0.97 | 21 | empty |
| 2 | 427 | 0.67 | 0.79 | 58 | empty |
| 3 | 251 | 0.53 | 0.76 | 37 | empty |
| 4 | 123 | 0.48 | 0.79 | 20 | empty |
| 5 | 135 | 0.44 | 0.76 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–C · 4237 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2211 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1628 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1159 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 939 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7VYM · Coxsackievirus B3 at PH7.4 (VP3-234E) 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 P78310
- Elsewhere: RCSB PDB 7VYM · PDBe 7VYM · UniProt P78310
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