SMTL ID : 9cfa.2 (2 other biounits)

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-CL04.1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain B: N.28, N.31 Chain C: D.144 No protein-ligand interaction detected (PLIP)

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

NAG.2: 8 residues within 4Å: Chain C: H.17, C.18, S.19, S.20, N.68, F.152, C.154 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.152 Hydrogen bonds: C:H.17, C:S.20 NAG.3: 6 residues within 4Å: Chain C: S.19, S.20, N.21, N.68, E.99 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiffner, T. et al., Diverse competitor B cell responses to a germline-targeting priming immunogen in human Ig loci transgenic mice. To Be Published

Release Date

2025-06-25

Peptides

Fab eOD-CL04.1 lambda light chain: A
Fab eOD-CL04.1 heavy chain: B
germline-targeting HIV-1 gp120 engineered outer domain eODgt8: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Fab eOD-CL04.1 lambda light chain

Fab eOD-CL04.1 heavy chain

germline-targeting HIV-1 gp120 engineered outer domain eODgt8

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