SMTL ID : 6ooo.1

Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-226.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.120, T.122, P.124, L.163, H.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 Water bridges: A:N.120 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 No protein-ligand interaction detected (PLIP) NAG.3: 9 residues within 4Å: Chain A: P.98, K.138, L.147, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:K.138, A:N.148, A:S.310 NAG.4: 3 residues within 4Å: Chain A: N.162, T.164, N.165 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.156 NAG.6: 7 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305, N.307, V.309 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.181, A:Y.200, A:Y.200, A:E.202, A:K.305 NAG.7: 2 residues within 4Å: Chain A: N.204, T.276 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: T.241, M.242, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.257 NAG.9: 2 residues within 4Å: Chain A: N.224, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 NAG.10: 4 residues within 4Å: Chain A: L.151, S.177, N.311 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.177, A:N.311 Water bridges: A:K.176, A:S.177

1 x MXJ: (3S,5R)-5-amino-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide(Non-covalent)

MXJ.11: 13 residues within 4Å: Chain A: V.141, S.142, T.143, E.239, T.244, F.245, N.246, F.251, N.288, M.289, W.290, G.292, G.294 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:F.251, A:W.290 Hydrogen bonds: A:N.288 pi-Stacking: A:W.290

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

EPE.12: 7 residues within 4Å: Chain A: L.11, C.13, H.31, A.32, Q.62, D.66, Y.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.11, A:Q.62 Salt bridges: A:D.66, A:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grenier, M.C. et al., Optimization of Small Molecules That Sensitize HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity. Acs Med.Chem.Lett. (2020)

Release Date

2020-03-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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