SMTL ID : 8gcz.1

Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with ZXC-I-090

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.120, T.122, S.160, L.163, H.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120, A:T.122, A:T.122 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.127 NAG.3: 10 residues within 4Å: Chain A: D.97, P.98, K.138, L.147, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:K.138, A:S.310 Water bridges: A:D.97, A:N.148, A:N.148 NAG.4: 4 residues within 4Å: Chain A: N.162, T.164, N.165 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.162 NAG.5: 7 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.176, Q.214, K.218 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.176 Hydrogen bonds: A:E.155, A:I.156 NAG.6: 6 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, N.307, V.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.183, A:Y.200 NAG.7: 3 residues within 4Å: Chain A: N.204, T.206, K.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.206, A:K.207 NAG.8: 5 residues within 4Å: Chain A: T.241, M.242, N.255, T.257 Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: N.224, N.225 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: L.151, S.177, N.311 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.177 NAG.11: 3 residues within 4Å: Chain A: P.232, N.261 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: T.164, N.324 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.324

1 x YZI: (3S,5S)-5-(aminomethyl)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide(Non-covalent)

YZI.13: 16 residues within 4Å: Chain A: V.141, S.142, T.143, D.237, E.239, T.244, F.245, F.251, I.287, N.288, M.289, W.290, G.292, T.293, G.336, M.338 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:F.251, A:I.287, A:N.288 Hydrogen bonds: A:D.237, A:D.237, A:N.288 pi-Stacking: A:W.290 Halogen bonds: A:T.244

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.14: 7 residues within 4Å: Chain A: L.11, C.13, H.31, A.32, Q.62, D.66, Y.103 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.66, A:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, S. et al., Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC. Viruses (2023)

Release Date

2023-06-07

Peptides

HIV-1 LM/HT Clade A/E CRF01 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 LM/HT Clade A/E CRF01 gp120 core

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