SMTL ID : 4jzz.1

Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 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 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.184, A:N.184, A:T.186, A:N.187, A:N.187 NAG.2: 4 residues within 4Å: Chain A: N.142, T.144, S.182, E.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.144, A:T.144 Water bridges: A:N.142, A:S.182 NAG.3: 3 residues within 4Å: Chain A: K.66, N.137, N.149 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.66 Water bridges: A:N.149, A:N.149 NAG.4: 10 residues within 4Å: Chain A: E.119, P.120, R.160, L.169, N.170, C.329, S.330, S.331 Ligands: NAG.8, NA.17 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.169 Hydrogen bonds: A:N.170, A:S.331 Water bridges: A:E.119, A:P.120, A:R.160, A:R.160, A:R.160, A:N.269 NAG.5: 7 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, E.198, Q.236, K.240 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:I.178, A:N.197, A:E.198 NAG.6: 6 residues within 4Å: Chain A: N.203, N.224, L.225, S.226, N.297, R.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.203, A:N.297, A:R.328, A:R.328 Water bridges: A:N.224 NAG.7: 2 residues within 4Å: Chain A: N.278, T.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.278, A:T.280 NAG.8: 5 residues within 4Å: Chain A: R.160, S.199, N.332 Ligands: NAG.4, IPA.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.199, A:N.332 Water bridges: A:S.199, A:S.199

6 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: V.264, T.265, N.278, S.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.264, A:S.279 NA.14: 6 residues within 4Å: Chain A: V.162, S.164, L.167, L.168, L.169, N.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.164, A:L.167, A:L.169, A:N.362 NA.15: 3 residues within 4Å: Chain A: P.255, S.256, V.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.256 NA.16: 4 residues within 4Å: Chain A: H.47, W.93, F.118, P.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.47 Water bridges: A:V.163 NA.17: 4 residues within 4Å: Chain A: F.118, P.120, N.269 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.269 Water bridges: A:N.269 NA.18: 3 residues within 4Å: Chain A: I.90, D.94, E.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.94

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

IPA.10: 3 residues within 4Å: Chain A: F.34, A.54, V.56 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.34 Water bridges: A:H.53, A:C.55 IPA.11: 5 residues within 4Å: Chain A: V.56, P.57, D.59, C.126, C.155 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.56, A:D.59 IPA.12: 5 residues within 4Å: Chain A: N.170, S.330, S.331, N.332 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332 IPA.13: 5 residues within 4Å: Chain A: V.25, W.26, L.67, E.72, L.134 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.67, A:L.134 Hydrogen bonds: A:W.26, A:E.72 Water bridges: A:K.371 IPA.19: 2 residues within 4Å: Chain A: P.261, K.305 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.261

1 x FLC: CITRATE ANION(Non-covalent)

FLC.20: 6 residues within 4Å: Chain A: R.219, R.303, I.304, K.305, Q.306, I.307 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.305 Hydrogen bonds: A:Q.306, A:I.307, A:I.307 Salt bridges: A:R.303

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 M48U1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
R

HIV-1 YU2 gp120 glycoprotein

CD4-MIMETIC MINIPROTEIN M48U1

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