SMTL ID : 6c6q.1

Crystal Structure of the Murine Norovirus VP1 P Domain in complex with the CD300lf Receptor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: M.1, N.236, A.237, F.238, T.239 Ligand excluded by PLIP EDO.2: 10 residues within 4Å: Chain A: P.18, S.56, C.60, R.164, V.166, P.167 Chain B: P.18, A.19, R.209 Ligands: EDO.5 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: Y.171, G.172, D.212, T.213 Chain D: V.40, P.41 Ligands: MG.11 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: Q.106, E.128, Y.171, I.211, T.213 Ligand excluded by PLIP EDO.5: 11 residues within 4Å: Chain A: E.110, V.166, P.167, R.168, R.209 Chain B: E.110, V.166, P.167, R.168, R.209 Ligands: EDO.2 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.10 Chain B: D.85, G.86, S.87 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: T.46, L.47, L.48, G.49, D.93, R.94 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: W.232 Chain B: M.1, D.3, W.232, N.236, F.238 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: Q.112, R.164 Chain B: Y.207, M.208, R.209, A.218 Ligands: CL.8 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.168 Chain B: V.124, T.125, T.126, V.150, L.156 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain B: F.69, Q.70, S.71, G.72, T.73, G.74, T.151, A.152, A.153 Chain C: D.3 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: Y.171, G.172, I.211, D.212 Chain C: V.40, P.41 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: P.5, I.7, E.228, S.231, W.232 Chain B: E.228, S.231, W.232, S.235 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: T.134, T.135, N.136 Chain C: C.37, R.43, S.44, C.45, K.46, T.47 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: G.28, W.29, Y.32 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: Q.38, G.39, S.84, D.85, A.86, G.87, I.88, Y.89 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: K.46, T.47, L.48, K.60, N.61 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: G.72, T.73 Chain C: Q.42, R.43, W.90, M.101, F.102 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain C: N.68 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain D: G.13, Q.14, G.17, S.18, L.19, L.81 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: T.73, Q.106, E.128, M.129, I.130, S.149 Chain D: Q.42, R.43 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain D: A.86, G.87, T.105, V.106, N.107, I.108 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain A: R.164 Chain B: A.19, P.20, Y.22, R.209 Ligands: EDO.13 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: A.19, R.209 Chain B: R.164 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 2 residues within 4Å: Chain A: D.138, D.182 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.138, A:D.182, H2O.2, H2O.3, H2O.5, H2O.7 MG.11: 4 residues within 4Å: Chain A: Q.210, D.212, D.215 Ligands: EDO.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.212, H2O.2, H2O.3, H2O.3, H2O.5 MG.18: 2 residues within 4Å: Chain B: D.138, D.182 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.138, B:D.182, H2O.13, H2O.13, H2O.16, H2O.18 MG.19: 3 residues within 4Å: Chain B: Q.210, D.212, D.215 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.212, H2O.12, H2O.13, H2O.14, H2O.15 MG.26: 6 residues within 4Å: Chain B: N.136, A.137, D.138 Chain C: K.95, G.97, D.99 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:K.95, C:G.97, C:D.99, B:N.136, H2O.18 MG.30: 6 residues within 4Å: Chain A: N.136, A.137, D.138 Chain D: K.95, G.97, D.99 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:N.136, D:K.95, D:G.97, D:D.99, H2O.8

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

Capsid protein VP1: AB
CMRF35-like molecule 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
F

Capsid protein VP1

CMRF35-like molecule 1

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