SMTL ID : 7jjc.4 (3 other biounits)

Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

1 x ARG- ALA- ARG: Spike protein S1(Non-covalent)

ARG-ALA-ARG.1: 8 residues within 4Å: Chain A: Y.36, W.40, T.55, D.59, S.85, E.87, T.88, Y.92 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.36, A:W.40 Hydrogen bonds: A:Y.36, A:Y.36, A:Y.36, A:T.55, A:T.55, A:S.85, A:T.88, A:Y.92, A:Y.92 Salt bridges: A:D.59

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

PEG.2: 1 residues within 4Å: Chain A: S.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.103, A:S.103

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.112, E.113, G.114, P.135, K.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.112, A:E.113, A:E.113, A:G.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daly, J.L. et al., Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science (2020)

Release Date

2020-10-28

Peptides

Neuropilin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Neuropilin-1

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