SMTL ID : 6onh.1

Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-031-A05.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.120, T.122, I.158, H.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.120, A:N.120 NAG.2: 3 residues within 4Å: Chain A: N.115, K.117, N.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117, A:N.127 NAG.3: 7 residues within 4Å: Chain A: K.138, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.138, A:N.148, A:S.310 Water bridges: A:D.97, A:D.97 NAG.4: 3 residues within 4Å: Chain A: N.162, T.164, N.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.164, A:N.165 Water bridges: A:N.162 NAG.5: 7 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, E.217, K.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.156, A:I.156, A:N.175 Water bridges: A:Q.214 NAG.6: 5 residues within 4Å: Chain A: E.179, N.181, E.202, K.305, V.309 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.181, A:K.305 Water bridges: A:N.307 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 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: 5 residues within 4Å: Chain A: N.148, L.151, S.177, N.311 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.177, A:N.311 Water bridges: A:S.177

1 x MWD: (3S)-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide(Non-covalent)

MWD.11: 14 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.335, G.336, D.337 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:T.244, A:F.251, A:N.288 Hydrogen bonds: A:N.288, A:G.336 pi-Stacking: A:W.290 Halogen bonds: A:T.244

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:Q.62, A:Q.62 Salt bridges: A:D.66, A:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, S. et al., A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity. J.Virol. (2019)

Release Date

2019-10-23

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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