SMTL ID : 8fly.1 (3 other biounits)

HIV-1 gp120 complex with BNM-III-170

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.118, T.120, P.122, I.156, S.158, L.161, H.220 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 NAG.2: 9 residues within 4Å: Chain A: P.96, K.136, L.145, N.146, N.244, R.246, C.309, N.310, S.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.311 NAG.3: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, E.174, K.212, E.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:E.216, A:E.216 NAG.4: 4 residues within 4Å: Chain A: T.239, T.240, N.253, S.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.240 Hydrogen bonds: A:N.253, A:S.255 Water bridges: A:N.253 NAG.5: 8 residues within 4Å: Chain A: E.229, P.230, S.255, D.256, N.259, T.270, G.271, R.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.256, A:N.259, A:R.272 NAG.6: 3 residues within 4Å: Chain A: N.160, T.162, N.163 No protein-ligand interaction detected (PLIP) NAG.8: 6 residues within 4Å: Chain A: E.203, S.204, N.207, Y.267, H.269, G.276 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.269 Hydrogen bonds: A:E.203, A:N.207

1 x 5VG: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide(Non-covalent)

5VG.7: 19 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, I.238, S.242, F.243, N.244, F.249, I.288, N.289, M.290, W.291, E.293, V.294, G.295, G.338, G.339, M.341 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.237, A:I.238, A:I.288 Hydrogen bonds: A:N.289, A:M.290, A:M.290, A:G.295, A:G.339 Water bridges: A:D.235, A:E.237, A:N.289, A:G.295 pi-Stacking: A:W.291 Halogen bonds: A:S.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fritschi, C.J. et al., Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-04-05

Peptides

Envelope glycoprotein gp120: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Envelope glycoprotein gp120

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