SMTL ID : 9dd7.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-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: 11 residues within 4Å: Chain A: N.141, E.379 Chain D: V.1, F.26, S.27, S.31, R.97, W.100, P.103, D.111, F.112 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.100, D:W.100, D:D.111 NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain B: N.141, E.379 Chain E: F.26, S.27, S.31, R.97, W.100, P.103, F.112 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.100, E:W.100 NAG-NAG-BMA-MAN-MAN.5: 8 residues within 4Å: Chain C: N.141, E.379 Chain F: F.26, S.27, R.97, W.100, P.103, F.112 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.100, F:W.100

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: 3 residues within 4Å: Chain B: N.398, Y.402, L.443 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.398, Y.402, L.443 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: N.430, A.431 Chain G: Y.52, S.67 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.52, G:Y.52 NAG.8: 4 residues within 4Å: Chain B: N.430, A.431 Chain H: Y.52, S.67 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.52 NAG.9: 5 residues within 4Å: Chain C: N.430, A.431 Chain I: Y.52, G.66, S.67 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.52

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
I

E
J

F
K

G
M

H
N

I
O

Glycoprotein B

D48 heavy chain

D48 light chain

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