SMTL ID : 6vsl.1

Crystal structure of a human fucosylated IgG1 Fc expressed in tobacco plants (Nicotiana benthamiana)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1: 18 residues within 4Å: Chain A: F.8, F.10, P.11, P.12, K.13, D.16, E.25, T.27, V.31, D.32, Q.62, Y.63, N.64, T.66, R.68, K.101 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:F.10, A:K.13, A:D.16, A:D.16, A:E.25, A:E.25, A:T.27 Water bridges: A:K.13, A:K.13, A:K.101 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2: 16 residues within 4Å: Chain B: F.8, F.10, P.11, P.12, K.13, E.25, T.27, V.29, V.31, D.32, Q.62, Y.63, N.64, T.66, R.68 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.63 Hydrogen bonds: B:F.10, B:K.13, B:K.13, B:E.25, B:E.25 Water bridges: B:D.16, B:T.23

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: G.4, P.5, S.6, V.7, I.99, K.101 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.99 Hydrogen bonds: A:S.6, A:V.7, A:K.101, A:K.101 MPD.4: 6 residues within 4Å: Chain B: P.5, S.6, V.7, I.99, E.100, K.101 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.99, B:K.101 Hydrogen bonds: B:S.6, B:V.7, B:K.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, S.P. et al., Enhanced Ability of Plant-Derived PGT121 Glycovariants To Eliminate HIV-1-Infected Cells. J.Virol. (2021)

Release Date

2021-02-17

Peptides

Immunoglobulin gamma-1 heavy chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Immunoglobulin gamma-1 heavy chain

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