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Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at pH 4.6
Analyse Crystal structure of the tetramerization domain of the glycoprotein gn (andes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YRQ
- Type
- protein + RNA
- Length
- 411 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope polyprotein; RNA (5'-R(*AP*UP*UP*UP*A)-3')
- UniProt
- Q9E006
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope polyprotein | protein | 99 | 25% helix, 42% strand | Q9E006 |
| D | Envelope polyprotein | protein | 102 | 25% helix, 36% strand | Q9E006 |
| E, F, G, H | RNA (5'-R(*AP*UP*UP*UP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, D, A
- BMA · beta-D-mannopyranose · sugar
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.80 | 0.82 | 75 | MPD |
| 2 | 80 | 0.32 | 0.74 | 19 | empty |
| 3 | 55 | 0.29 | 0.75 | 12 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1047 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1046 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1036 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1021 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 459 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6YRQ · Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at… · the same entry in another collection · chain A against A, 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 Q9E006
- Elsewhere: RCSB PDB 6YRQ · PDBe 6YRQ · UniProt Q9E006
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