SMTL ID : 4b3v.3 (2 other biounits)

Crystal structure of the Rubella virus glycoprotein E1 in its post-fusion form crystallized in presence of 20mM of Calcium Acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: Q.168, S.175, N.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.168, A:S.175, A:S.175, A:N.177 NAG.2: 2 residues within 4Å: Chain A: A.72, N.76 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.72 Hydrogen bonds: A:N.76

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA.3: 3 residues within 4Å: Chain A: T.430, A.431, V.432 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: G.93, G.94, Y.95, A.96, Q.97, L.98, Y.101 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.94, A:A.96, A:Q.97, A:L.98 Water bridges: A:Y.101, A:Y.101 GOL.5: 4 residues within 4Å: Chain A: Y.95, Y.101, Y.112 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101, A:Y.101 GOL.6: 5 residues within 4Å: Chain A: T.347, G.348, P.355, A.356, L.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.347 GOL.7: 3 residues within 4Å: Chain A: R.256, L.257, D.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.257, A:D.262 Water bridges: A:L.257 GOL.8: 3 residues within 4Å: Chain A: S.100, Y.101, Y.108 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain A: N.88, T.135, D.136, T.137 Ligands: CA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.88, A:T.137 Water bridges: A:D.127 ACT.10: 3 residues within 4Å: Chain A: Y.90, S.92, D.136 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.90

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: N.88, A.89, D.136, T.137 Ligands: ACT.9 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:A.89, A:D.136, A:T.137, H2O.4, ACT.9

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 5 residues within 4Å: Chain A: G.63, W.65, V.66, P.67, T.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.63, A:T.68 PEG.13: 9 residues within 4Å: Chain A: E.52, I.53, P.54, T.55, D.56, G.61, W.65, Y.90, Q.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.55, A:D.56, A:G.61, A:Y.90, A:Q.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubois, R.M. et al., Functional and Evolutionary Insight from the Crystal Structure of Rubella Virus Protein E1. Nature (2013)

Release Date

2013-01-09

Peptides

E1 ENVELOPE GLYCOPROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

E1 ENVELOPE GLYCOPROTEIN

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