MolNFT v1 · #171056 · protein + RNA
Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at pH 4.6
6YRQ · Envelope polyprotein: “Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at pH 4.6”. X-ray diffraction, 2 ligands (NAG, BMA), 3 pockets (best druggability 0.80). MolNFT v1 #171056 on GenesisL1: 3D…
- 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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