SMTL ID : 7n3k.2 (3 other biounits)

Oridonin-bound SARS-CoV-2 Nsp9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x ODN: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one(Non-covalent)(Covalent)

ODN.1: 10 residues within 4Å: Chain A: E.90, P.91, P.92, C.93, F.110, R.119 Chain B: F.16, N.21, N.22, L.117 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.119 Hydrophobic interactions: B:F.16, B:F.16, B:F.16, B:N.22, B:L.117 ODN.2: 8 residues within 4Å: Chain A: F.16, L.117 Chain B: E.90, P.91, P.92, C.93, F.110, R.119 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.16, A:F.16, A:F.16, A:L.117, B:P.91 Hydrogen bonds: B:E.90, B:E.90, B:R.119

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: N.116 Chain B: N.115, N.116, L.117 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.116, B:N.116, B:L.117, A:N.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Littler, D.R. et al., A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein. J.Biol.Chem. (2021)

Release Date

2021-10-27

Peptides

Non-structural protein 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Non-structural protein 9

Related Entries With Identical Sequence