SMTL ID : 5ies.1

Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.16 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.100, S.102, S.104, D.106 Chain B: L.52, E.61 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.61, A:S.100, A:G.101, A:S.104, A:S.104 GOL.2: 7 residues within 4Å: Chain A: G.42 Chain B: D.9, V.91, Y.93, G.102, G.103, K.105 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.93 Water bridges: A:G.42 GOL.3: 5 residues within 4Å: Chain B: L.15, A.86, S.170, K.171, S.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.171, B:S.173

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

NAG.4: 5 residues within 4Å: Chain C: S.16, S.17, N.18, E.96 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.96 NAG.5: 10 residues within 4Å: Chain C: H.14, C.15, S.16, S.17, V.57, N.65, F.149, N.150, C.151 Ligands: NAG.4 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.149 Hydrogen bonds: C:H.14, C:S.17 Water bridges: C:H.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jardine, J.G. et al., HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Science (2016)

Release Date

2016-04-06

Peptides

VRC01cHuGL2 Fab heavy chain: A
VRC01cHuGL2 Fab light chain: B
Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

VRC01cHuGL2 Fab heavy chain

VRC01cHuGL2 Fab light chain

Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8

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