SMTL ID : 8dcq.1

CRYSTAL STRUCTURE OF HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH YIR-821

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.120, T.122, P.124, I.158, L.163, H.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.115, A:N.127 NAG.3: 8 residues within 4Å: Chain A: D.97, P.98, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.138, A:N.148, A:S.310 NAG.4: 1 residues within 4Å: Chain A: N.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.162 NAG.5: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, K.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.156, A:K.218, A:K.218 NAG.6: 6 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305, V.309 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.181, A:T.183, A:Y.200, A:K.305 NAG.7: 4 residues within 4Å: Chain A: N.204, K.207, G.275, T.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.207 NAG.8: 4 residues within 4Å: Chain A: L.238, M.242, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.238 NAG.9: 3 residues within 4Å: Chain A: E.221, N.224, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 NAG.10: 5 residues within 4Å: Chain A: K.138, N.148, S.177, N.311 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.177, A:N.311

1 x R5K: N~1~-{(3R)-1-[2-(5-carbamimidamidopentanamido)ethyl]-1-azaspiro[5.5]undecan-3-yl}-N~2~-(4-chlorophenyl)ethanediamide(Non-covalent)

R5K.11: 14 residues within 4Å: Chain A: V.141, T.143, E.239, I.240, T.244, F.245, N.246, F.251, N.288, M.289, W.290, G.336, D.337, M.338 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.143, A:T.244, A:F.251 Hydrogen bonds: A:N.288, A:G.336 pi-Stacking: A:W.290

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

EPE.12: 8 residues within 4Å: Chain A: L.11, F.12, 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:H.31 Salt bridges: A:D.66, A:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, K. et al., Characterization of a Novel CD4 Mimetic Compound YIR-821 against HIV-1 Clinical Isolates. J.Virol. (2023)

Release Date

2023-01-11

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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