SMTL ID : 4dku.1 (1 other biounit)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-09027

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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.118, T.120, P.122, I.156, S.158, H.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.120 NAG.2: 2 residues within 4Å: Chain A: K.124, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.3: 10 residues within 4Å: Chain A: D.95, P.96, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 NAG.5: 5 residues within 4Å: Chain A: E.153, I.154, N.173, Q.212, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:I.154, A:N.173 NAG.6: 3 residues within 4Å: Chain A: N.179, Y.198, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:Y.198, A:E.200 NAG.7: 6 residues within 4Å: Chain A: N.202, G.203, T.204, K.205, G.273, T.274 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.222, N.223 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309

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

EPE.11: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.64, A:D.64

1 x 0KU: N-(4-chlorophenyl)-N'-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide(Non-covalent)

0KU.12: 18 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, I.238, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, Q.289, G.290, G.333, G.334, N.335 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.139, A:T.141, A:E.237, A:I.238, A:F.249, A:I.285 Hydrogen bonds: A:N.286, A:G.334 pi-Stacking: A:W.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Curreli, F. et al., Binding mode characterization of NBD series CD4-mimetic HIV-1 entry inhibitors by X-ray structure and resistance study. Antimicrob. Agents Chemother. (2014)

Release Date

2013-03-20

Peptides

HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 gp120 core

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