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Conformational variability of a picornavirus capsid: pH-dependent structural changes of mengo virus related to its host receptor attachment site and disassembly
Analyse Conformational variability of a picornavirus capsid: pH-dependent structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MEC
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mengo virus coat protein (subunit VP1); Mengo virus coat protein (subunit VP2)
- UniProt
- P12296
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Mengo virus coat protein (subunit VP1) | protein | 274 | 5% helix, 25% strand | P12296 |
| 2 | Mengo virus coat protein (subunit VP2) | protein | 256 | 10% helix, 38% strand | P12296 |
| 3 | Mengo virus coat protein (subunit VP1) | protein | 231 | 6% helix, 32% strand | P12296 |
| 4 | Mengo virus coat protein (subunit VP1) | protein | 62 | 6% helix, 0% strand | P12296 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains 1, 2, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.77 | 0.79 | 77 | empty |
| 2 | 645 | 0.72 | 0.79 | 73 | empty |
| 3 | 55 | 0.71 | 0.98 | 22 | empty |
| 4 | 246 | 0.53 | 0.76 | 31 | PO4 |
| 5 | 130 | 0.46 | 0.78 | 23 | empty |
Interfaces
6 interfaces between chains.
- 1–2 · 2352 Ų buried · 35 hydrogen bonds · protein-protein
- 1–3 · 1432 Ų buried · 14 hydrogen bonds · protein-protein
- 2–3 · 813 Ų buried · 9 hydrogen bonds · protein-protein
- 1–4 · 610 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 501 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1MEC · Conformational variability of a picornavirus capsid: pH-dependent structural changes of… · the same entry in another collection · chain 2 against 2, TM-score 1.00
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 P12296
- Elsewhere: RCSB PDB 1MEC · PDBe 1MEC · UniProt P12296
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