SMTL ID : 5kzc.1 (2 other biounits)

Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at position N276, in complex with broadly neutralizing antibody VRC01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN.1: 10 residues within 4Å: Chain B: N.79, F.80 Chain C: Y.28, G.29, S.30, R.64, W.65, G.66, Y.69, Y.89 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.29, C:R.64, C:R.64, C:Y.69

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

NAG.2: 4 residues within 4Å: Chain B: S.16, S.17, N.18, E.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.96 NAG.3: 7 residues within 4Å: Chain B: H.14, C.15, S.17, V.57, N.65, N.151, C.152 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.57 Hydrogen bonds: B:H.14, B:S.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jardine, J.G. et al., Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design. Plos Pathog. (2016)

Release Date

2016-08-10

Peptides

VRC01 Fab heavy chain: A
Engineered outer domain of gp120: B
VRC01 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
L

VRC01 Fab heavy chain

Engineered outer domain of gp120

VRC01 Fab light chain

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