SMTL ID : 6e48.1

Crystal Structure of the Murine Norovirus VP1 P domain in complex with the CD300lf Receptor and Lithocholic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 4OA: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid(Non-covalent)

4OA.1: 9 residues within 4Å: Chain A: A.19, P.20, Y.22, Y.207, R.209, A.218 Chain B: Q.112, R.162, R.164 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.22, B:R.164 Hydrogen bonds: A:Y.22, A:Y.22, A:R.209 Water bridges: B:R.164 Salt bridges: B:R.164 4OA.5: 10 residues within 4Å: Chain A: Q.112, R.162, R.164 Chain B: W.17, A.19, P.20, Y.22, Y.207, R.209, A.218 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.22 Water bridges: B:Y.207, B:R.209, A:R.164 Salt bridges: B:R.209, A:R.164 Hydrophobic interactions: A:R.164

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: Q.210, D.212, D.215, E.219 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.212, H2O.2, H2O.9, H2O.9, H2O.10 CA.3: 2 residues within 4Å: Chain A: D.138, D.182 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.138, A:D.182, H2O.7, H2O.8, H2O.11 CA.6: 6 residues within 4Å: Chain B: N.136, A.137, D.138 Chain D: K.95, G.97, D.99 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:K.95, D:G.97, D:D.99, B:N.136, B:D.138, H2O.27 CA.7: 2 residues within 4Å: Chain B: D.138, D.182 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.138, B:D.182, H2O.20, H2O.22, H2O.28 CA.8: 4 residues within 4Å: Chain B: Q.210, D.212, D.215, E.219 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.212, H2O.18, H2O.19, H2O.22, H2O.26 CA.9: 7 residues within 4Å: Chain A: N.136, A.137, D.138 Chain C: K.95, G.96, G.97, D.99 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:K.95, C:G.97, C:D.99, A:N.136, A:D.138, H2O.11

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

EDO.4: 10 residues within 4Å: Chain A: A.65, Y.67, Q.112, T.113, E.114, V.159, D.160, G.161, R.162, V.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.67, A:Y.67 Water bridges: A:E.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nelson, C.A. et al., Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-12

Peptides

VP1 P domain: AB
CMRF35-like molecule 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
G

VP1 P domain

CMRF35-like molecule 1

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