SMTL ID : 9cu4.1

KSHV glycoprotein B ectodomain, postfusion form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.1: 9 residues within 4Å: Chain A: Y.93, S.96, H.97, F.105, S.107, M.108, N.126, V.220, H.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.105 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3: 9 residues within 4Å: Chain B: Y.93, S.96, H.97, F.105, S.107, M.108, N.126, V.220, H.223 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.105 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.5: 9 residues within 4Å: Chain C: Y.93, S.96, H.97, F.105, S.107, M.108, N.126, V.220, H.223 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.105

3 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: N.201, S.256 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.201, S.256 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.201, S.256 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: A.573, N.575 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: L.221, N.222, N.239 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.302, D.305 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: I.314, N.315, Y.337 Ligands: NAG.11 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.315, T.316, N.319 Ligands: NAG.10 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Y.39, N.332, S.352 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Y.10, R.545, N.546 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.561 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: A.573, N.575 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: L.221, N.222, N.239 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.302, D.305 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: I.314, N.315, Y.337 Ligands: NAG.19 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.315, T.316, N.319 Ligands: NAG.18 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: Y.39, N.332, S.352 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.10, R.545, N.546 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.561 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: A.573, N.575 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: L.221, N.222, N.239 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.302, D.305 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: I.314, N.315, Y.337 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.315, T.316, N.319 Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: Y.39, N.332, S.352 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: Y.10, R.545, N.546 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.561 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, F. et al., Structure of the Kaposi's sarcoma-associated herpesvirus gB in post-fusion conformation. J.Virol. (2025)

Release Date

2025-01-08

Peptides

ORF8: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ORF8