SMTL ID : 4dw4.1 (1 other biounit)

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with 5'-UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- MAN- BMA: alpha-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(Post Translational Modification)

NAG-NAG-BMA-MAN-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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.87, A:E.90, A:N.85 Water bridges: A:P.91 NAG-NAG-BMA-MAN-BMA.4: 3 residues within 4Å: Chain A: N.13, R.20, F.23 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain A: G.26, N.28, A.149, G.150, I.151 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)

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

NAG.5: 4 residues within 4Å: Chain A: H.57, L.94, N.97, A.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.57 Water bridges: A:H.57, A:N.97

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

SO4.6: 3 residues within 4Å: Chain A: T.49, D.50, T.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.50, A:T.51, A:T.51 SO4.7: 2 residues within 4Å: Chain A: H.76, N.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.79 Water bridges: A:H.76 Salt bridges: A:H.76

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.8: 8 residues within 4Å: Chain A: I.5, H.32, W.35, H.76, E.77, K.80, H.81, R.131 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.35 Hydrogen bonds: A:W.35, A:R.131 Water bridges: A:Q.7, A:H.76, A:K.80 Salt bridges: A:H.32, A:H.76, A:K.80, A:H.81 pi-Stacking: A:W.35 U5P.9: 7 residues within 4Å: Chain A: N.9, I.18, Q.19, H.32, A.62, L.73, Q.129 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.62 Hydrogen bonds: A:N.9, A:N.9, A:Q.19, A:Q.129

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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