SMTL ID : 8f9z.1

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-14204, an HIV-1 gp120 antagonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

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

NAG.1: 9 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, R.157, S.158, L.161, H.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.118, A:H.220 Water bridges: A:N.118, A:N.118, A:S.158, A:S.158 NAG.2: 11 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, F.243, N.244, C.306, V.307, S.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.308 Water bridges: A:D.95, A:D.95, A:N.146 NAG.3: 3 residues within 4Å: Chain A: N.160, T.162, N.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:N.163 Water bridges: A:N.163 NAG.4: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:I.154, A:Q.212 Water bridges: A:N.173 NAG.5: 8 residues within 4Å: Chain A: E.177, N.179, T.181, Y.198, E.200, K.303, N.305, V.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:T.181, A:E.200, A:K.303 NAG.6: 5 residues within 4Å: Chain A: L.236, T.239, M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:N.253

1 x XKW: (5M)-N-{(1S)-2-amino-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl}-5-[5-(trifluoromethyl)pyridin-2-yl]-1H-pyrrole-2-carboxamide(Non-covalent)

XKW.7: 18 residues within 4Å: Chain A: W.69, V.139, S.140, T.141, D.235, E.237, I.238, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, G.290, G.334, I.336 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:I.238, A:W.288 Hydrogen bonds: A:N.286, A:W.288 Water bridges: A:N.286, A:N.286, A:M.287 pi-Stacking: A:W.288 Halogen bonds: A:V.139

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

EPE.8: 10 residues within 4Å: Chain A: T.8, L.9, F.10, C.11, W.26, H.29, A.30, Q.60, D.64, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.9 Salt bridges: A:D.64, A:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Curreli, F. et al., Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists. Int J Mol Sci (2022)

Release Date

2023-01-11

Peptides

HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 gp120 core

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