SMTL ID : 4dw5.1 (1 other biounit)

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a non-cleavable CpU dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA-BMA.1: 9 residues within 4Å: Chain A: N.4, P.36, N.85, W.86, Y.87, N.88, E.90, P.91, L.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.87, A:N.85

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: L.94, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: L.95, K.98, T.99, N.102 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: G.26, N.28, A.149, I.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 NAG.5: 2 residues within 4Å: Chain A: R.25, N.67 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.13, R.20, F.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.23 Hydrogen bonds: A:N.13 Water bridges: A:R.20

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: R.72, H.76, N.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.79 Salt bridges: A:R.72, A:H.76 SO4.8: 2 residues within 4Å: Chain A: R.72, R.75 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.75, A:R.75 Salt bridges: A:R.72, A:R.75 SO4.9: 6 residues within 4Å: Chain A: H.32, W.35, H.76, E.77, K.80, H.81 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.80 Salt bridges: A:H.32, A:H.76, A:K.80, A:H.81

1 x CSQ: O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} hydrogen (R)-phosphorothioate(Non-covalent)

CSQ.10: 10 residues within 4Å: Chain A: N.9, Q.19, H.32, A.62, S.63, R.72, L.73, H.76, Q.129 Ligands: CSV.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.62, A:R.72 Hydrogen bonds: A:N.9, A:N.9, A:Q.19, A:R.72, A:Q.129

1 x CSV: O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} hydrogen (S)-phosphorothioate(Non-covalent)

CSV.11: 10 residues within 4Å: Chain A: N.9, I.18, Q.19, H.32, A.62, S.63, R.72, L.73, Q.129 Ligands: CSQ.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.62 Hydrogen bonds: A:N.9, A:N.9, A:Q.19, A:R.72, A:Q.129

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 5 residues within 4Å: Chain A: H.46, T.49, D.50, T.51, E.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.49, A:D.50, A:T.51, A:T.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krey, T. et al., Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity. Structure (2012)

Release Date

2012-05-23

Peptides

E(rns) glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E(rns) glycoprotein

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