SMTL ID : 4ka2.1

Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.184, T.186, N.187 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.184, A:N.187, A:N.187, A:N.187 NAG.2: 5 residues within 4Å: Chain A: N.142, T.144, G.145, P.146, S.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.144 Water bridges: A:S.182 NAG.3: 4 residues within 4Å: Chain A: K.66, N.137, K.139, N.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.66, A:K.139 NAG.4: 11 residues within 4Å: Chain A: E.119, P.120, R.160, V.162, L.169, N.170, F.268, C.329, S.330, S.331 Ligands: NAG.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.162, A:L.169 Hydrogen bonds: A:E.119, A:S.331 Water bridges: A:R.160, A:R.160, A:N.170, A:N.170, A:N.269, A:G.271 NAG.5: 7 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, E.198, Q.236, K.240 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:E.177, A:E.177, A:I.178, A:N.197, A:E.198, A:E.198 Water bridges: A:K.240 NAG.6: 8 residues within 4Å: Chain A: V.201, N.203, N.224, L.225, S.226, N.297, R.328, S.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:S.330 Water bridges: A:N.203 NAG.7: 2 residues within 4Å: Chain A: N.278, T.280 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.278, A:N.278, A:N.278 NAG.8: 5 residues within 4Å: Chain A: N.170, L.173, S.199, N.332 Ligands: NAG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.199, A:N.332 Water bridges: A:R.160, A:S.199, A:S.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morellato-Castillo, L. et al., Interfacial Cavity Filling To Optimize CD4-Mimetic Miniprotein Interactions with HIV-1 Surface Glycoprotein. J.Med.Chem. (2013)

Release Date

2013-06-19

Peptides

HIV-1 YU2 gp120: A
M48U12: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
R

HIV-1 YU2 gp120

M48U12

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