SMTL ID : 9dd9.1

Cryo-EM structure of neutralizing human antibody D48 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E

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 D: G.25, F.26, S.27, S.31, R.97, V.99, W.100, P.103, D.111, F.112 Chain G: Q.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 13 residues within 4Å: Chain B: N.141, E.379 Chain E: G.25, F.26, S.27, S.31, R.97, V.99, W.100, P.103, D.111, F.112 Chain H: Q.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 13 residues within 4Å: Chain C: N.141, E.379 Chain F: G.25, F.26, S.27, S.31, R.97, V.99, W.100, P.103, D.111, F.112 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: 2 residues within 4Å: Chain A: N.398, L.443 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.398, L.443 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.398, L.443 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 G: Y.52, S.67 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.674 Chain B: R.136 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.674, B:R.136 NAG.9: 3 residues within 4Å: Chain B: N.430 Chain H: Y.52, S.67 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: N.674 Chain C: R.136 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.674, C:R.136 NAG.11: 3 residues within 4Å: Chain C: 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 C: N.674 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.674, A:R.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roark, R.S. et al., Herpes simplex virus 1 evades prefusion gB neutralization. To Be Published

Release Date

2025-09-10

Peptides

Glycoprotein B: ABC
D48 heavy chain: DEF
D48 light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

F
J

G
L

H
M

I
N

Glycoprotein B

D48 heavy chain

D48 light chain

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