SMTL ID : 6vlk.1 (1 other biounit)

A varicella-zoster virus glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN.1: 7 residues within 4Å: Chain A: I.241, A.242, K.244, H.254, T.255, T.256, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 7 residues within 4Å: Chain B: I.241, A.242, K.244, H.254, T.255, T.256, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 7 residues within 4Å: Chain C: I.241, A.242, K.244, H.254, T.255, T.256, N.257 No protein-ligand interaction detected (PLIP)

3 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.2: 4 residues within 4Å: Chain A: N.686, T.688 Chain B: K.394, R.534 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain B: N.686, T.688 Chain C: K.394, R.534 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 4 residues within 4Å: Chain A: K.394, R.534 Chain C: N.686, T.688 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.620, S.622 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.622, A:S.622 NAG.6: 2 residues within 4Å: Chain B: N.620, S.622 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.622, B:S.622 NAG.9: 2 residues within 4Å: Chain C: N.620, S.622 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.622, C:S.622

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliver, S.L. et al., A glycoprotein B-neutralizing antibody structure at 2.8 angstrom uncovers a critical domain for herpesvirus fusion initiation. Nat Commun (2020)

Release Date

2020-07-15

Peptides

Envelope glycoprotein B: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Envelope glycoprotein B

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