SMTL ID : 3tyg.1

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3)

Coordinates

PDB Format

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- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-MAN-MAN.1: 19 residues within 4Å: Chain A: T.2, T.4, T.100, R.116, H.119, N.121 Chain B: V.89, G.90, N.91, W.92, D.93 Chain C: Y.59, W.60, W.64, T.65, Y.66, H.67, P.69, K.72 1 PLIP interactions: 1 interactions with chain A, Hydrogen bonds: A:R.116

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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.2: 12 residues within 4Å: Chain A: N.104, T.106, I.112 Chain C: S.28, A.30, C.32, H.55, C.56, A.57, R.62, T.81, P.82 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.55, C:H.55, C:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pejchal, R. et al., A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield. Science (2011)

Release Date

2011-10-19

Peptides

Envelope glycoprotein gp160: A
PGT128 light chain, Ig lambda-2 chain C regions: B
PGT128 heavy chain, Ig gamma-1 chain C region: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Envelope glycoprotein gp160

PGT128 light chain, Ig lambda-2 chain C regions

PGT128 heavy chain, Ig gamma-1 chain C region

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