Research workbench
Cryo-EM structure of coxsackievirus B1 virion in complex with car
Analyse Cryo-EM structure of coxsackievirus B1 virion in complex with car in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DPZ
- Type
- protein
- Length
- 917 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion protein 1; VP2; VP3; Capsid protein VP4; Coxsackievirus and adenovirus receptor
- UniProt
- W8GTF7, A0A2S0RQC2, L7UV52, A0A2S1FMR1, P78310
- Pockets
- 19 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 7% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Virion protein 1 | protein | 267 | 8% helix, 26% strand | W8GTF7 |
| 2 | VP2 | protein | 252 | 9% helix, 30% strand | A0A2S0RQC2 |
| 3 | VP3 | protein | 237 | 6% helix, 29% strand | L7UV52 |
| 4 | Capsid protein VP4 | protein | 50 | 6% helix, 14% strand | A0A2S1FMR1 |
| K | Coxsackievirus and adenovirus receptor | protein | 111 | 3% helix, 40% strand | P78310 |
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.77 | 0.83 | 60 | empty |
| 2 | 69 | 0.72 | 0.97 | 27 | empty |
| 3 | 52 | 0.70 | 0.98 | 22 | empty |
| 4 | 222 | 0.54 | 0.77 | 24 | empty |
| 5 | 183 | 0.52 | 0.78 | 24 | empty |
Interfaces
8 interfaces between chains.
- 1–3 · 4087 Ų buried · 47 hydrogen bonds · protein-protein
- 1–2 · 2132 Ų buried · 21 hydrogen bonds · protein-protein
- 2–3 · 1649 Ų buried · 10 hydrogen bonds · protein-protein
- 1–4 · 1103 Ų buried · 11 hydrogen bonds · protein-protein
- 3–4 · 847 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DPZ · Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P78310 · AlphaFold monomer V2.0 prediction for coxsackievirus and adenovirus receptor (P78310) · a predicted model of the same protein · chain K against A, TM-score 0.95
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 W8GTF7
- Every structure of UniProt A0A2S0RQC2
- Every structure of UniProt L7UV52
- Every structure of UniProt A0A2S1FMR1
- Every structure of UniProt P78310
- Elsewhere: RCSB PDB 7DPZ · PDBe 7DPZ · UniProt W8GTF7 · UniProt A0A2S0RQC2 · UniProt L7UV52 · UniProt A0A2S1FMR1 · UniProt P78310
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