SMTL ID : 4i53.1 (1 other biounit)

Crystal structure of clade C1086 HIV-1 gp120 core in complex with DMJ-II-121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x 1C1: amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium(Non-covalent)

1C1.1: 19 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, S.242, F.243, N.244, F.249, I.288, N.289, M.290, W.291, E.293, V.294, G.295, G.338, G.339, D.340, M.341 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.249, A:I.288 Hydrogen bonds: A:N.289, A:E.293, A:G.295, A:G.339 Water bridges: A:E.237, A:E.237 pi-Stacking: A:W.291 Halogen bonds: A:S.242

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

NAG.2: 6 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, L.161, H.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:S.158 NAG.3: 8 residues within 4Å: Chain A: P.96, K.136, L.145, N.146, N.244, C.309, N.310, S.311 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.311 Water bridges: A:D.95, A:D.95, A:N.310 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: 5 residues within 4Å: Chain A: E.153, I.154, N.173, K.212, E.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.154, A:E.174, A:E.174, A:E.216, A:E.216 NAG.6: 5 residues within 4Å: Chain A: E.203, S.204, N.207, Y.267, G.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.269 NAG.7: 5 residues within 4Å: Chain A: L.236, T.239, T.240, N.253, S.255 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.236, A:T.240 Hydrogen bonds: A:N.253, A:S.255 Water bridges: A:T.239, A:N.253, A:N.253 NAG.8: 8 residues within 4Å: Chain A: E.229, P.230, S.255, D.256, N.259, T.270, G.271, R.272 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.230 Hydrogen bonds: A:D.256, A:D.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lalonde, J.M. et al., Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett (2013)

Release Date

2013-05-29

Peptides

HIV-1 glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 glycoprotein

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