SMTL ID : 4dku.2 (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

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

NAG.1: 3 residues within 4Å: Chain A: N.118, T.120, P.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.118 NAG.2: 3 residues within 4Å: Chain A: H.42, N.113, N.125 No protein-ligand interaction detected (PLIP) NAG.3: 8 residues within 4Å: Chain A: K.136, L.145, N.146, R.246, C.306, V.307, S.308 Ligands: NAG.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:R.246, A:R.246 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160, A:T.162 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.154, A:Q.212, A:K.216, A:K.216 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:E.200, A:E.200 NAG.7: 5 residues within 4Å: Chain A: N.202, G.203, K.205, G.273, T.274 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:T.255, A:T.255 NAG.9: 3 residues within 4Å: Chain A: S.175, N.309 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.175

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

EPE.10: 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.11: 18 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, I.238, S.242, F.243, F.249, I.285, N.286, M.287, W.288, Q.289, G.290, G.333, G.334, N.335, I.336 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:I.238, A:W.288 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
B

HIV-1 gp120 core

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