Research workbench
Structural refinement and analysis of mengo virus
Analyse Structural refinement and analysis of mengo virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MEV
- Type
- protein
- Length
- 806 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); Mengo…
- UniProt
- P12296
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Mengo virus coat protein (subunit VP1) | protein | 268 | 7% helix, 25% strand | P12296 |
| 2 | Mengo virus coat protein (subunit VP2) | protein | 249 | 11% helix, 39% strand | P12296 |
| 3 | Mengo virus coat protein (subunit VP3) | protein | 231 | 7% helix, 32% strand | P12296 |
| 4 | Mengo virus coat protein (subunit VP4) | protein | 58 | 7% helix, 0% strand | P12296 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains 1, 2, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.81 | 0.85 | 62 | PO4 |
| 2 | 833 | 0.75 | 0.79 | 77 | empty |
| 3 | 160 | 0.49 | 0.78 | 26 | empty |
| 4 | 180 | 0.48 | 0.76 | 24 | empty |
| 5 | 112 | 0.44 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- 1–2 · 2207 Ų buried · 33 hydrogen bonds · protein-protein
- 1–3 · 1401 Ų buried · 18 hydrogen bonds · protein-protein
- 2–3 · 763 Ų buried · 8 hydrogen bonds · protein-protein
- 3–4 · 523 Ų buried · 3 hydrogen bonds · protein-protein
- 1–4 · 467 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2MEV · Structural refinement and analysis of mengo virus · the same entry in another collection · chain 3 against 3, 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 2MEV · PDBe 2MEV · UniProt P12296
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