SMTL ID : 6oz2.1

Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.120, G.123, P.124, S.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.120 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.42, A:N.127 NAG.3: 10 residues within 4Å: Chain A: D.97, P.98, K.138, V.140, N.148, N.246, C.247, R.248, V.309, S.310 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.140 Hydrogen bonds: A:D.97, A:K.138, A:N.148, A:R.248, A:S.310 NAG.4: 5 residues within 4Å: Chain A: N.162, T.164 Chain C: N.27, Y.28, F.87 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:N.27, C:F.87 Hydrogen bonds: C:Y.28, A:N.162, A:T.164 NAG.5: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, K.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.155, A:I.156, A:K.218, A:K.218 NAG.6: 4 residues within 4Å: Chain A: E.179, N.181, E.202, N.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.181 NAG.7: 3 residues within 4Å: Chain A: N.204, T.206, K.207 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: P.232, N.255, T.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.255, A:T.257 NAG.9: 4 residues within 4Å: Chain A: Q.258, N.261, C.264, C.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.261, A:C.273 NAG.10: 3 residues within 4Å: Chain A: N.148, S.177, N.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.177 NAG.11: 2 residues within 4Å: Chain A: N.225, T.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Near-Pan-neutralizing, Plasma Deconvoluted Antibody N49P6 Mimics Host Receptor CD4 in Its Quaternary Interactions with the HIV-1 Envelope Trimer. Mbio (2021)

Release Date

2020-08-19

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
N49P6 antibody Fab heavy chain: B
N49P6 antibody Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

N49P6 antibody Fab heavy chain

N49P6 antibody Fab light chain

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