SMTL ID : 4rfn.2 (1 other biounit)

Crystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in complex with HIV-1 CLADE A/E GP120 and M48

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 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: 6 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, L.161, H.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:T.120 NAG.2: 5 residues within 4Å: Chain A: H.42, N.113, K.115, N.125, E.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.42, A:E.151 NAG.3: 10 residues within 4Å: Chain A: P.96, K.136, V.138, L.145, N.146, N.244, R.246, C.306, V.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:V.307, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.162 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.174 Hydrogen bonds: A:I.154, A:Q.212 NAG.6: 4 residues within 4Å: Chain A: E.177, N.179, T.181, K.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.181 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, N.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.204 NAG.8: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain A: Q.256, N.259, C.262, G.270, C.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.270

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 93TH057 (H375S) GP120: A
FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4: B
FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4: C
T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

HIV-1 CLADE A/E 93TH057 (H375S) GP120

FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4

FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4

T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48

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