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

Crystal structure of unliganded HIV-1 clade C strain C1086 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, I.156, L.161, H.220 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 NAG.2: 8 residues within 4Å: Chain A: D.95, K.136, L.145, N.146, C.309, N.310, S.311 Ligands: NAG.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:D.95, A:K.136, A:N.146, A:S.311 NAG.3: 3 residues within 4Å: Chain A: N.160, T.162, N.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:T.162, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:E.174, A:E.174, A:E.216, A:E.216 NAG.5: 4 residues within 4Å: Chain A: E.203, S.204, N.207, Y.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.203, A:E.203, A:Y.267 NAG.6: 3 residues within 4Å: Chain A: T.239, N.253, S.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:N.253, A:S.255 NAG.7: 5 residues within 4Å: Chain A: P.230, S.255, D.256, N.259, T.270 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.230 Hydrogen bonds: A:D.256, A:D.256, A:T.270 NAG.8: 3 residues within 4Å: Chain A: S.175, N.312 Ligands: NAG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.175, A:N.312 Water bridges: A:S.175, A:N.312

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 clade C1086 gp120

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