SMTL ID : 8w2e.1

SARS-CoV-2 M protein dimer in complex with JNJ-9676 and Fab-B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x 01: (6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide

01.1: 18 residues within 4Å: Chain A: W.55, W.58, L.87, V.88, M.91, W.92, Y.95, F.96, S.99, F.112, P.114, E.115, T.116, N.117 Chain B: I.32, C.33, Q.36, F.37 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.58, A:W.58, A:L.87, A:V.88, A:Y.95, B:I.32, B:F.37 Hydrogen bonds: A:S.99, A:N.117 pi-Stacking: A:W.58, A:Y.95 01.2: 19 residues within 4Å: Chain A: L.29, I.32, C.33, Q.36, F.37 Chain B: W.55, W.58, V.88, M.91, W.92, Y.95, F.96, S.99, F.112, N.113, P.114, E.115, T.116, N.117 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.88, B:Y.95, B:Y.95, B:P.114, A:L.29, A:I.32, A:Q.36, A:F.37 Hydrogen bonds: B:N.117 pi-Stacking: B:W.58, B:W.58, B:Y.95 Halogen bonds: A:I.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Y. et al., SARS-CoV-2 M protein dimer in complex with JNJ-9676 and Fab-B. To Be Published

Release Date

2025-01-29

Peptides

Membrane protein: AB
Fab B Heavy Chain: CE
Fab B Light Chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

Membrane

We predict this structure to be a membrane protein.
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Membrane protein

Fab B Heavy Chain

Fab B Light Chain