SMTL ID : 6h6l.2 (1 other biounit)

Murine norovirus protruding domain (CW3 strain) in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.139, D.183 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.139, A:D.183, H2O.1, H2O.2, H2O.2 MG.2: 4 residues within 4Å: Chain A: Q.211, D.213, A.218, E.220 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:E.220, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: D.139, D.183 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.139, H2O.3, H2O.4, H2O.5, H2O.5 MG.7: 3 residues within 4Å: Chain B: Q.211, D.213, E.220 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:E.220, H2O.3, H2O.4

2 x CHO: GLYCOCHENODEOXYCHOLIC ACID(Non-covalent)

CHO.3: 15 residues within 4Å: Chain A: W.18, P.19, A.20, Y.23, Y.208, M.209, R.210 Chain B: A.63, I.83, Q.85, G.87, Q.113, R.163, V.164, R.165 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.83, B:Q.113, B:R.163, A:Y.23, A:Y.208, A:Y.208 Water bridges: B:R.165 Salt bridges: B:R.165, A:R.210 Hydrogen bonds: A:Y.208, A:Y.208, A:R.210 CHO.5: 15 residues within 4Å: Chain A: A.63, I.83, Q.85, G.87, Q.113, R.163, V.164, R.165 Chain B: W.18, P.19, A.20, Y.23, Y.208, M.209, R.210 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:I.83, A:R.163, A:R.165, B:Y.23, B:Y.23, B:Y.208 Salt bridges: A:R.165, B:R.210 Hydrogen bonds: B:Y.208, B:Y.208, B:R.210 Water bridges: B:R.210, B:R.210

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: N.137, D.139 Chain C: K.94, G.96, D.98 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.98 NA.8: 5 residues within 4Å: Chain B: N.137, D.139 Chain D: K.94, G.96, D.98 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.94, D:D.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kilic, T. et al., Crystal structures of murine norovirus protruding domain with conjugated bile acid reveal a novel binding pocket. To Be Published

Release Date

2019-08-14

Peptides

Capsid protein: AB
CMRF35-like molecule 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
G

D
H

Capsid protein

CMRF35-like molecule 1

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