SMTL ID : 8gd3.1

Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with DL-I-101

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.120, T.122, P.124, I.158, L.163, H.222 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.2: 4 residues within 4Å: Chain A: E.42, N.115, K.117, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.42, A:K.117, A:N.127 NAG.3: 11 residues within 4Å: Chain A: P.98, K.138, V.140, L.147, N.148, N.246, R.248, C.308, V.309, S.310 Ligands: NAG.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.140, A:L.147 Hydrogen bonds: A:K.138, A:N.148, A:R.248, A:S.310 NAG.4: 4 residues within 4Å: Chain A: N.162, T.164, N.165 Ligands: NAG.10 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.155, A:I.156, A:K.218, A:K.218 NAG.6: 4 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:Y.200, A:E.202 Water bridges: A:N.307 NAG.7: 3 residues within 4Å: Chain A: N.204, T.206, K.207 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:N.255 NAG.9: 4 residues within 4Å: Chain A: L.151, S.177, N.311 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.177, A:N.311 NAG.10: 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 EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 7 residues within 4Å: Chain A: L.11, C.13, H.31, A.32, Q.62, D.66, Y.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.62 Salt bridges: A:D.66, A:D.66

1 x Z1Z: (3S,5R)-N-(4-chloro-3-fluorophenyl)-1-(4-glycylpiperazine-1-carbonyl)-5-(hydroxymethyl)piperidine-3-carboxamide(Non-covalent)

Z1Z.12: 17 residues within 4Å: Chain A: V.141, S.142, T.143, D.237, E.239, S.244, F.245, F.251, I.287, N.288, M.289, W.290, Q.291, G.292, T.293, G.336, M.338 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:E.239, A:F.251, A:I.287, A:N.288 Hydrogen bonds: A:D.237, A:D.237, A:N.288, A:R.339 pi-Stacking: A:W.290 Halogen bonds: A:S.244

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain A: N.118, F.119, N.120, K.126 Ligands: NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.120, A:N.120, A:K.126 Water bridges: A:N.120

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/HS clade A/E CRF01 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 LM/HS clade A/E CRF01 gp120 core

Related Entries With Identical Sequence