SMTL ID : 4jkp.1

Restricting HIV-1 Pathways for Escape using Rationally-Designed Anti-HIV-1 Antibodies

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: 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.1: 9 residues within 4Å: Chain A: N.160, L.161 Chain C: Y.28, G.29, R.64, W.65, G.66, Y.89 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.64, C:R.64

1 x NAG- NAG- BMA- MAN- MAN: 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.2: 11 residues within 4Å: Chain A: K.91, S.93, D.95, V.138, N.146, N.244, R.246, N.305, C.306, V.307, S.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.246, A:R.246

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, E.215, K.216 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.215

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

NAG.4: 2 residues within 4Å: Chain A: N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:E.200 NAG.6: 4 residues within 4Å: Chain A: N.118, T.120, S.158 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118, A:T.120 NAG.7: 2 residues within 4Å: Chain A: N.202, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.8: 5 residues within 4Å: Chain C: I.20, S.63, W.65, D.68, N.70 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diskin, R. et al., Restricting HIV-1 pathways for escape using rationally designed anti-HIV-1 antibodies. J.Exp.Med. (2013)

Release Date

2013-05-15

Peptides

gp120: A
Heavy chain of antibody 45-46M2: B
Light chain of antibody 45-46M2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

gp120

Heavy chain of antibody 45-46M2

Light chain of antibody 45-46M2

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