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

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with 2'-UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.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:W.86, A:N.88, A:N.88, A:N.85

1 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: 3 residues within 4Å: Chain A: H.57, L.94, N.97 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: G.26, N.28, A.149, I.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.28 Water bridges: A:G.26, A:N.28 NAG.4: 5 residues within 4Å: Chain A: L.95, K.98, T.99, N.102, L.109 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.95, A:K.98 Hydrogen bonds: A:K.98, A:K.98, A:N.102 Water bridges: A:T.6, A:T.99

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

SO4.5: 6 residues within 4Å: Chain A: H.32, W.35, H.76, E.77, K.80, H.81 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.32, A:H.76, A:K.80, A:H.81 SO4.6: 3 residues within 4Å: Chain A: T.49, D.50, T.51 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.49, A:D.50, A:D.50, A:D.50, A:T.51, A:T.51, A:T.51 SO4.7: 2 residues within 4Å: Chain A: H.76, N.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.79 Salt bridges: A:H.76

1 x U2P: PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER(Non-covalent)

U2P.8: 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
B

E(rns) glycoprotein

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