SMTL ID : 4dvk.2 (1 other biounit)

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 strain NCP-7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- BMA- MAN- MAN: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)-alpha-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-MAN-MAN.1: 9 residues within 4Å: Chain A: N.2, P.34, N.83, W.84, Y.85, N.86, E.88, P.89, L.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.83

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: 4 residues within 4Å: Chain A: A.53, L.92, N.95, A.99 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: L.93, K.96, T.97, N.100, L.107 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.24, N.26, A.147, I.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.24, A:N.26 NAG.5: 2 residues within 4Å: Chain A: R.23, N.65 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.23, A:N.65 NAG.6: 3 residues within 4Å: Chain A: N.11, R.18, F.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:N.11 Water bridges: A:R.18, A:R.18

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

SO4.7: 7 residues within 4Å: Chain A: H.30, W.33, H.74, E.75, K.78, H.79 Ligands: SO4.10 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.75, A:E.75 Salt bridges: A:H.30, A:H.74, A:K.78, A:H.79 SO4.8: 2 residues within 4Å: Chain A: S.61, K.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.61 Water bridges: A:K.63 Salt bridges: A:K.63 SO4.9: 3 residues within 4Å: Chain A: Y.116, R.118, K.139 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.118, A:K.139 SO4.10: 3 residues within 4Å: Chain A: H.74, K.78 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.74, A:K.78 SO4.11: 1 residues within 4Å: Chain A: H.44 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.44, A:H.44 Salt bridges: A:H.44 SO4.12: 2 residues within 4Å: Chain A: R.70, R.73 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.70 Salt bridges: A:R.70, A:R.73 SO4.13: 6 residues within 4Å: Chain A: N.7, I.16, H.30, A.60, L.71, Q.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.7, A:N.7 Water bridges: A:H.30 Salt bridges: A:H.30

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
B

E(rns) glycoprotein

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