SMTL ID : 4k0a.1

Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.184 NAG.2: 6 residues within 4Å: Chain A: N.142, T.144, G.145, P.146, S.182, F.185 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.185 Hydrogen bonds: A:T.144, A:T.144 Water bridges: A:N.142, A:N.142, A:S.182 NAG.3: 4 residues within 4Å: Chain A: K.66, N.137, K.139, N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.139 NAG.4: 12 residues within 4Å: Chain A: E.119, P.120, R.160, V.162, L.169, N.170, F.268, N.269, C.329, S.330, S.331 Ligands: NAG.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.162, A:L.169 Hydrogen bonds: A:E.119, A:N.170, A:S.331 Water bridges: A:R.160, A:R.160 NAG.5: 7 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, E.198, Q.236, K.240 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:I.178, A:N.197, A:E.198, A:E.198 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:N.203, A:R.328, A:R.328 Water bridges: A:N.224 NAG.7: 6 residues within 4Å: Chain A: V.264, T.265, N.278, T.280, Q.281, P.301 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.264 Hydrogen bonds: A:T.280 Water bridges: A:N.278, A:Q.281 NAG.8: 6 residues within 4Å: Chain A: R.160, N.170, L.173, S.199, N.332 Ligands: NAG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.199, A:S.199, A:N.332 Water bridges: A:S.199

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.9: 6 residues within 4Å: Chain A: V.25, W.26, L.67, V.70, E.72, L.134 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.25 Hydrogen bonds: A:W.26, A:W.26 IPA.10: 5 residues within 4Å: Chain A: F.34, D.59, P.60, C.126, Q.154 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.34 Water bridges: A:T.58 IPA.11: 4 residues within 4Å: Chain A: F.34, H.53, A.54, V.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.54 Water bridges: A:C.35 IPA.12: 7 residues within 4Å: Chain A: W.77, K.78, N.79, V.82, E.83, R.360, R.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.77, A:N.79, A:R.364, A:R.364

1 x FLC: CITRATE ANION(Non-covalent)

FLC.13: 5 residues within 4Å: Chain A: R.219, R.303, K.305, Q.306, I.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.306, A:I.307 Salt bridges: A:R.303, A:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acharya, P. et al., Structural Basis for Highly Effective HIV-1 Neutralization by CD4-Mimetic Miniproteins Revealed by 1.5 A Cocrystal Structure of gp120 and M48U1. Structure (2013)

Release Date

2013-06-12

Peptides

HIV-1 YU2 gp120 glycoprotein: A
CD4-MIMETIC MINIPROTEIN M48U7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
R

HIV-1 YU2 gp120 glycoprotein

CD4-MIMETIC MINIPROTEIN M48U7

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