Research workbench
Coxsackievirus B3 (VP3-234Q) incubation with CD55 at PH7.4
Analyse Coxsackievirus B3 (VP3-234Q) incubation with CD55 at PH7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VY5
- Type
- protein
- Length
- 942 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Genome polyprotein…
- UniProt
- P03313, P08174
- Ligands
- PLM
- Pockets
- 12 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 268 | 9% helix, 31% strand | P03313 |
| B | Capsid protein VP2 | protein | 256 | 8% helix, 34% strand | P03313 |
| C | Capsid protein VP3 | protein | 238 | 10% helix, 28% strand | P03313 |
| D | Genome polyprotein | protein | 57 | 0% helix, 16% strand | P03313 |
| E | Complement decay-accelerating factor | protein | 123 | 4% helix, 36% strand | P08174 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 522 | 0.78 | 0.85 | 66 | PLM |
| 2 | 328 | 0.65 | 0.81 | 42 | empty |
| 3 | 170 | 0.56 | 0.81 | 38 | empty |
| 4 | 159 | 0.49 | 0.77 | 21 | empty |
| 5 | 136 | 0.47 | 0.78 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4314 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2171 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1676 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1165 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7VY5 · Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 · the same entry in another collection · chain A against A, TM-score 1.00
- P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 P08174
- Elsewhere: RCSB PDB 7VY5 · PDBe 7VY5 · UniProt P03313 · UniProt P08174
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