SMTL ID : 7qik.1

SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x SER- SER- ARG- ASN- SEP- THR- PRO- GLY: SER-SER-ARG-ASN-SEP-THR-PRO-GLY(Non-covalent)

SER-SER-ARG-ASN-SEP-THR-PRO-GLY.1: 15 residues within 4Å: Chain B: S.48, K.52, R.59, K.125, R.132, Y.133, G.174, L.177, N.178, V.181, E.185, L.225, D.228, N.229, L.232 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.225, B:L.232 Hydrogen bonds: B:R.59, B:K.125, B:K.125, B:R.132, B:E.136, B:N.178, B:N.178, B:N.229, B:N.229, B:N.229 Water bridges: B:K.52, B:K.52, B:E.136 Salt bridges: B:K.52, B:R.59, B:R.132, B:E.185 SER-SER-ARG-ASN-SEP-THR-PRO-GLY.2: 13 residues within 4Å: Chain A: R.59, K.125, R.132, Y.133, E.136, G.174, L.177, N.178, V.181, E.185, L.225, N.229, L.232 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.177, A:L.225 Hydrogen bonds: A:R.59, A:K.125, A:K.125, A:R.132, A:E.136, A:N.178, A:N.178, A:N.229, A:N.229 Water bridges: A:E.136 Salt bridges: A:R.59, A:R.132, A:E.185

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: E.20, R.21, Y.22, E.23, D.24, N.53, V.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.22, A:E.23, A:D.24, A:D.24, A:N.53 PEG.4: 6 residues within 4Å: Chain A: D.148, R.151, S.152, Q.155, F.179, H.183 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.151, A:F.179 Hydrogen bonds: A:D.148 PEG.9: 6 residues within 4Å: Chain A: E.94 Chain B: E.20, R.21, Y.22, E.23, D.24 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.22, B:E.23, B:D.24 Water bridges: B:E.23, A:E.23 PEG.10: 4 residues within 4Å: Chain B: Y.51, G.97, V.98, T.101 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.51, B:Y.51, B:V.98

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.96, D.100, L.134, I.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.100, A:D.100 Water bridges: A:Q.96, A:Q.96 GOL.11: 5 residues within 4Å: Chain B: Q.96, D.100, L.134, D.142, I.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.142

4 x BR: BROMIDE ION(Non-covalent)

BR.6: 5 residues within 4Å: Chain A: K.12, F.28 Chain B: E.86, Y.87, K.90 Ligand excluded by PLIP BR.7: 5 residues within 4Å: Chain A: A.138, T.139, G.140, D.142, K.143 Ligand excluded by PLIP BR.8: 2 residues within 4Å: Chain A: Q.155, M.158 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain A: E.86, K.90 Chain B: K.12 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 5 residues within 4Å: Chain B: Y.184, E.185, N.188, S.189, P.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tugaeva, K.V. et al., Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J.Mol.Biol. (2023)

Release Date

2021-12-29

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

14-3-3 protein sigma

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