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MolNFT v1 · #171041 · protein + RNA

Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at pH 7.5

6YRB · Envelope polyprotein: “Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at pH 7.5”. X-ray diffraction, 4 ligands (NAG, BMA, FUC). MolNFT v1 #171041 on GenesisL1: 3D structure, binding sites and…

PDB
6YRB
Type
protein + RNA
Length
205 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Envelope polyprotein; RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
UniProt
Q9E006
Ligands
NAG, BMA, FUC, IOD

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 42% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEnvelope polyproteinprotein10025% helix, 41% strandQ9E006
BEnvelope polyproteinprotein9925% helix, 42% strandQ9E006
C, DRNA (5'-D(*())-R(P*UP*UP*UP*())-3')rna3——

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
  • BMA · beta-D-mannopyranose · sugar
  • FUC · alpha-L-fucopyranose · sugar · chains A
  • IOD · Iodide ion · ion · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

2 interfaces between chains.

  • B–C · 456 Ų buried · 12 hydrogen bonds · protein-nucleic
  • A–D · 438 Ų buried · 10 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

  • 6YRB · 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

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