Research workbench
Cryo-EM structure of Coxsackievirus B1 pre-A particle in complex with nAb 2E6 (CVB1-pre-A:2E6)
Analyse Cryo-EM structure of Coxsackievirus B1 pre-A particle in complex with nAb 2E6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X2I
- Type
- protein
- Length
- 1,040 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.29
- Source
- Coxsackievirus B1; Mus musculus
- Molecule
- 2E6 light chain; 2E6 heavy chain; Virion protein 1; VP2; VP3; Capsid protein VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- W8GTF7, A0A2S0RQC2, L7UV52, A0A2S1FMR1
- Pockets
- 13 · best druggability 0.76
Structure
electron microscopy · resolution 3.29 · 6 distinct chains · 6% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 2E6 light chain | protein | 107 | 0% helix, 42% strand | — |
| H | 2E6 heavy chain | protein | 119 | 3% helix, 43% strand | — |
| A | Virion protein 1 | protein | 267 | 8% helix, 29% strand | W8GTF7 |
| B | VP2 | protein | 252 | 8% helix, 34% strand | A0A2S0RQC2 |
| C | VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 238 | 4% helix, 28% strand | L7UV52 |
| D | Capsid protein VP4 | protein | 57 | 11% helix, 9% strand | A0A2S1FMR1 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.76 | 0.84 | 68 | empty |
| 2 | 266 | 0.64 | 0.81 | 41 | empty |
| 3 | 250 | 0.57 | 0.79 | 32 | empty |
| 4 | 114 | 0.51 | 0.81 | 25 | empty |
| 5 | 146 | 0.47 | 0.77 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4234 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2126 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1621 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1144 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 885 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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
- Elsewhere: RCSB PDB 7X2I · PDBe 7X2I · UniProt W8GTF7 · UniProt A0A2S0RQC2 · UniProt L7UV52 · UniProt A0A2S1FMR1
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