SMTL ID : 8enw.2 (1 other biounit)

Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x VAL- LYS- LEU- HIS- TYR- GLU: Clientized spike tail peptide(Non-covalent)

VAL-LYS-LEU-HIS-TYR-GLU.1: 16 residues within 4Å: Chain A: R.16, K.18, Y.34, R.60, D.99, Y.100, R.102, D.118, H.142, F.143, M.145, L.162, N.189, D.207, N.231, R.273 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.100 Hydrogen bonds: A:Y.34, A:R.60, A:R.60, A:R.102, A:R.102, A:D.118, A:D.207 Water bridges: A:R.16, A:K.18, A:D.207, A:N.231 Salt bridges: A:R.16, A:R.16, A:K.18, A:R.60, A:R.273

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: P.151, D.192, Y.193, P.195, V.236, F.237, P.239, T.279 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 EDO.3: 8 residues within 4Å: Chain A: Y.190, D.192, V.236, F.237, I.277, A.278, T.279 Ligands: EDO.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.279, A:T.279 Water bridges: A:D.21, A:D.21, A:T.279 EDO.4: 4 residues within 4Å: Chain A: D.15, R.16, Y.34, S.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.15, A:D.15, A:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, D. et al., A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Nat Commun (2023)

Release Date

2024-01-31

Peptides

Coatomer subunit beta': A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Coatomer subunit beta'

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