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

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, S.158, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118, A:T.120 NAG.2: 4 residues within 4Å: Chain A: D.114, K.115, K.124, N.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.124 Hydrogen bonds: A:K.115, A:N.125 NAG.3: 7 residues within 4Å: Chain A: L.145, N.146, N.244, C.306, V.307, S.308 Ligands: NAG.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:S.308 Water bridges: A:D.95 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.152, E.153, I.154, N.173, K.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:I.154, A:N.173 Water bridges: A:Q.212, A:Q.212 NAG.6: 2 residues within 4Å: Chain A: N.179, E.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:E.200 Water bridges: A:T.181, A:N.305 NAG.7: 6 residues within 4Å: Chain A: N.202, T.204, K.205, N.272, G.273, T.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.272 NAG.8: 2 residues within 4Å: Chain A: N.222, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.9: 3 residues within 4Å: Chain A: T.239, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 3 residues within 4Å: Chain A: Q.256, N.259, T.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:T.261 NAG.11: 6 residues within 4Å: Chain A: K.136, N.146, L.149, S.175, N.309 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 Water bridges: A:S.175, A:S.175

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

EPE.12: 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 0KW: N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide(Non-covalent)

0KW.13: 19 residues within 4Å: Chain A: 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, 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:I.285 Hydrogen bonds: A:N.286, A:G.334 Water bridges: A:Q.62 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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