SMTL ID : 6e47.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-2-2-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.138, E.179, D.182 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.138, A:D.182, H2O.1, H2O.4, H2O.4, H2O.5 MG.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.1, H2O.1, H2O.1, H2O.4 MG.11: 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.9, H2O.11, H2O.12 MG.12: 6 residues within 4Å: Chain B: Q.210, D.212, D.215, A.217, E.219 Ligands: EDO.13 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.212, H2O.8, H2O.8, H2O.9, H2O.11 MG.19: 6 residues within 4Å: Chain A: N.136, A.137, D.138 Chain C: K.94, G.96, D.98 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:K.94, C:G.96, C:D.98, A:N.136, A:D.138, H2O.6 MG.27: 7 residues within 4Å: Chain B: N.136, A.137, D.138 Chain D: K.94, G.96, D.98 Ligands: EDO.29 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:K.94, D:G.96, B:N.136, B:D.138, H2O.18

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

EDO.3: 7 residues within 4Å: Chain A: P.31, P.34, Q.35, W.36, D.175, T.176, I.177 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Q.143, N.181, L.184 Ligand excluded by PLIP EDO.5: 10 residues within 4Å: Chain A: R.16, L.30, W.36, F.173, D.175, R.203, R.205, A.220, I.221, D.222 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: Y.67, K.68, F.69, E.75, S.155, L.156, D.157, L.158 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.216, A.217, A.218 Chain B: Q.112, E.114, L.122 Ligands: CHO.10, EDO.15 Ligand excluded by PLIP EDO.8: 10 residues within 4Å: Chain A: P.5, I.7, E.228, S.231, W.232 Chain B: P.5, I.7, E.228, S.231, W.232 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: Y.171, G.172, D.212, T.213 Chain D: V.39 Ligands: MG.12 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: Y.67, K.68, F.69, E.75, S.155, L.156, D.157, L.158 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain B: A.65, Y.67, Q.112, T.113, E.114, V.159, D.160, G.161, R.162, V.163 Ligands: EDO.7 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain B: I.177, P.178, E.179, Y.180, N.181, L.184, L.185, V.186, L.188 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain B: R.16, L.30, W.36, F.173, D.175, R.203, R.205, A.220, I.221, D.222 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: A.214, D.215 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: N.136 Chain C: Y.34, T.46, E.49, T.93, D.98 Ligands: EDO.25 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain C: L.56, S.63, R.65, T.74, T.76 Ligands: EDO.26 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain C: G.27, W.28, Y.31 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: Y.31, K.32, A.52, T.93 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Q.70, V.76, T.78, F.147 Chain C: K.94, G.96, L.97 Ligand excluded by PLIP EDO.25: 9 residues within 4Å: Chain A: T.134, T.135, N.136 Chain C: C.36, R.42, S.43, C.44, T.46 Ligands: EDO.20 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: L.56, R.65 Ligands: EDO.21 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain D: G.27, W.28, Y.31 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: N.136 Chain D: Y.34, T.46, E.49, T.93, D.98 Ligands: MG.27 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain D: A.85, G.86, I.87, T.104, V.105, N.106, I.107 Ligand excluded by PLIP

2 x CHO: GLYCOCHENODEOXYCHOLIC ACID(Non-covalent)

CHO.9: 18 residues within 4Å: Chain A: A.62, A.63, I.82, E.83, Q.84, D.85, G.86, Q.112, R.162, V.163, R.164 Chain B: W.17, A.19, Y.22, Y.207, M.208, R.209, A.218 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Q.112, A:R.162, B:Y.22, B:Y.22, B:Y.207, B:Y.207 Hydrogen bonds: A:Q.112, B:W.17, B:R.209 Water bridges: A:R.164, A:R.164, B:R.209, B:R.209 Salt bridges: A:R.164, B:R.209 CHO.10: 21 residues within 4Å: Chain A: W.17, A.19, Y.22, Y.207, M.208, R.209, A.218 Chain B: A.62, A.63, E.64, I.82, E.83, Q.84, D.85, G.86, Q.112, R.162, V.163, R.164, V.166 Ligands: EDO.7 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.22, A:Y.22, A:Y.207, B:A.62, B:Q.112, B:R.162 Hydrogen bonds: A:W.17, A:R.209, B:Q.112, B:R.162, B:R.162 Water bridges: A:R.209, A:R.209, A:R.209, A:R.209 Salt bridges: A:R.209, B:R.164

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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