Research workbench
Crystal structure of the envelope glycoprotein complex of maporal virus in a prefusion conformation
Analyse Crystal structure of the envelope glycoprotein complex of maporal virus in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y62
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope POLYPROTEIN,ENVELOPE polyprotein
- UniProt
- Q5MYC0
- Ligands
- NAG, BMA, MAN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 352 | 13% helix, 44% strand | Q5MYC0 |
| B | Envelope POLYPROTEIN,ENVELOPE polyprotein | protein | 419 | 6% helix, 55% strand | Q5MYC0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.75 | 0.79 | 100 | empty |
| 2 | 56 | 0.58 | 0.90 | 20 | empty |
| 3 | 180 | 0.57 | 0.81 | 32 | empty |
| 4 | 137 | 0.50 | 0.80 | 20 | empty |
| 5 | 100 | 0.41 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1674 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y62 · Crystal structure of the envelope glycoprotein complex of Maporal virus in a prefusion… · the same entry in another collection · chain B against B, 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 Q5MYC0
- Elsewhere: RCSB PDB 6Y62 · PDBe 6Y62 · UniProt Q5MYC0
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