SMTL ID : 9dd8.1

Cryo-EM structure of neutralizing human antibody D48 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

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: 13 residues within 4Å: Chain A: N.141, E.379 Chain B: G.26, F.27, S.28, S.32, R.98, V.100, W.101, P.104, D.112, F.113 Chain C: Q.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 13 residues within 4Å: Chain D: N.141, E.379 Chain E: G.26, F.27, S.28, S.32, R.98, V.100, W.101, P.104, D.112, F.113 Chain F: Q.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 13 residues within 4Å: Chain G: N.141, E.379 Chain H: G.26, F.27, S.28, S.32, R.98, V.100, W.101, P.104, D.112, F.113 Chain I: Q.55 No protein-ligand interaction detected (PLIP)

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: 1 residues within 4Å: Chain A: N.398 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain D: N.398 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain G: N.398 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: N.430 Chain C: Y.52, S.67 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.674 Chain D: R.136 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.674, D:R.136 NAG.9: 3 residues within 4Å: Chain D: N.430 Chain F: Y.52, S.67 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain D: N.674 Chain G: R.136 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:R.136, D:N.674 NAG.11: 3 residues within 4Å: Chain G: N.430 Chain I: Y.52, S.67 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: R.136 Chain G: N.674 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:N.674, A:R.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roark, R.S. et al., Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B. Nat Microbiol (2025)

Release Date

2025-09-10

Peptides

Glycoprotein B: ADG
D48 heavy chain: BEH
D48 light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
I

H
J

C
L

F
M

I
N

Glycoprotein B

D48 heavy chain

D48 light chain

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