SMTL ID : 3tgs.1 (1 other biounit)

Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, L.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 NAG.2: 9 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, N.146, C.309, N.310, S.311 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:S.311 NAG.3: 3 residues within 4Å: Chain A: N.160, T.162, N.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.160, A:T.162, A:T.162 Water bridges: A:N.163 NAG.4: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, E.174, K.212, E.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.154, A:E.174, A:K.212, A:E.216 NAG.5: 5 residues within 4Å: Chain A: E.203, S.204, N.207, Y.267, H.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.267 Hydrogen bonds: A:E.203 NAG.6: 4 residues within 4Å: Chain A: T.239, T.240, N.253, S.255 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.240 Hydrogen bonds: A:N.253, A:S.255 NAG.8: 6 residues within 4Å: Chain A: E.229, P.230, S.255, D.256, N.259, T.270 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.230 Hydrogen bonds: A:D.256 NAG.9: 6 residues within 4Å: Chain A: N.146, S.175, N.312 Chain B: E.174, K.212 Ligands: NAG.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.174, B:K.212, A:S.175, A:N.312 NAG.10: 4 residues within 4Å: Chain B: N.118, T.120, P.122, S.158 No protein-ligand interaction detected (PLIP) NAG.12: 8 residues within 4Å: Chain B: D.95, K.136, V.138, N.146, N.244, C.309, N.310, S.311 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.95, B:K.136, B:N.146, B:S.311, B:S.311 NAG.13: 7 residues within 4Å: Chain A: N.310 Chain B: E.152, E.153, I.154, N.173, E.174, E.216 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.154, B:E.174, B:E.216, B:E.216 NAG.14: 2 residues within 4Å: Chain B: N.253, S.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.253 Water bridges: B:S.255 NAG.15: 5 residues within 4Å: Chain B: P.230, D.256, N.259, T.270, G.271 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.230 Hydrogen bonds: B:D.256

2 x 03G: N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide(Non-covalent)

03G.7: 14 residues within 4Å: Chain A: V.139, E.237, S.242, F.243, N.244, F.249, I.288, N.289, M.290, W.291, E.293, V.294, G.339, M.341 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.139, A:F.249, A:I.288, A:V.294 Hydrogen bonds: A:N.289, A:G.339 pi-Stacking: A:W.291 03G.11: 16 residues within 4Å: Chain B: V.139, 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.339, D.340, M.341 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.139, B:F.249, B:I.288, B:W.291, B:V.294, B:D.340 Hydrogen bonds: B:N.289, B:G.339 pi-Stacking: B:W.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, Y.D. et al., Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-04-04

Peptides

HIV-1 clade C1086 gp120 core: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 clade C1086 gp120 core

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