SMTL ID : 4jy4.1

Crystal structure of human Fab PGT121, a broadly reactive and potent HIV-1 neutralizing antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN- FUC: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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(Non-functional Binders)

NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-FUC.1: 4 residues within 4Å: Chain A: Q.5, N.124 Chain B: G.33, Q.34 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.34

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain B: E.78, T.101, T.103, G.141, Y.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.141 GOL.4: 5 residues within 4Å: Chain B: D.87, S.88, V.90, P.91, T.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.88, B:V.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Julien, J.P. et al., Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. Plos Pathog. (2013)

Release Date

2013-05-15

Peptides

PGT121 heavy chain: A
PGT121 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

PGT121 heavy chain

PGT121 light chain

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