SMTL ID : 4rfo.1

Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, P.122, S.158, L.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:P.122 NAG.2: 3 residues within 4Å: Chain A: N.113, K.115, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.115 NAG.3: 8 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, C.306, S.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:D.95, A:K.136, A:N.146, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160, A:T.162 NAG.5: 5 residues within 4Å: Chain A: E.153, I.154, N.173, Q.212, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.154 NAG.6: 5 residues within 4Å: Chain A: N.179, Y.198, E.200, K.303, N.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.303 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:T.204, A:K.205 NAG.8: 3 residues within 4Å: Chain A: M.240, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:C.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gohain, N. et al., Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1. J.Virol. (2015)

Release Date

2015-07-15

Peptides

HIV-1 clade A/E gp120: A
m48u1 CD4 mimetic peptide: B
N60-i3 Fab heavy chain: C
N60-i3 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
N

C
H

D
L

HIV-1 clade A/E gp120

m48u1 CD4 mimetic peptide

N60-i3 Fab heavy chain

N60-i3 Fab light chain

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