SMTL ID : 5n7m.1

Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-functional Binders)

GLC-GAL-FUC.1: 8 residues within 4Å: Chain A: D.103, H.105, Q.118, D.120, W.151, S.153, P.154, S.156 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.105, A:Q.118, A:D.120, A:S.153, A:S.153 Water bridges: B:S.114 GLC-GAL-FUC.2: 9 residues within 4Å: Chain A: S.114 Chain B: D.103, H.105, Q.118, D.120, W.151, S.153, P.154, S.156 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.118, B:D.120, B:D.103, B:H.105, B:S.153, B:S.153 Water bridges: B:D.103, B:S.156, A:S.114

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

NA.3: 3 residues within 4Å: Chain A: F.128, N.170, G.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.170 NA.11: 3 residues within 4Å: Chain B: F.128, N.170, G.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.172

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

EDO.4: 9 residues within 4Å: Chain A: S.219, H.220, S.223 Chain B: P.10, L.12, E.216, S.219, H.220 Ligands: EDO.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.219, B:H.220 Water bridges: A:H.220, A:S.223 EDO.5: 3 residues within 4Å: Chain A: N.11, P.240, V.278 No protein-ligand interaction detected (PLIP) EDO.6: 9 residues within 4Å: Chain A: Q.42, G.54, E.89, G.90, P.91, H.180, L.181, A.182 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.42, A:G.54, A:E.89, A:A.182 EDO.7: 6 residues within 4Å: Chain A: L.52, V.58, A.222 Chain B: L.12, P.13 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: V.53, G.54, A.182 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.54 EDO.9: 7 residues within 4Å: Chain A: K.200, M.201, G.205, A.206, Y.207, N.208 Chain B: F.111 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.112 Hydrogen bonds: A:Y.207 EDO.10: 4 residues within 4Å: Chain A: G.50, R.51, L.52 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.52 EDO.12: 9 residues within 4Å: Chain A: P.10, L.12, E.216, S.219, H.220 Chain B: S.219, H.220, S.223 Ligands: EDO.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.220, B:S.219, B:H.220 EDO.13: 4 residues within 4Å: Chain B: N.11, P.240, V.276, V.278 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A. et al., Human norovirus inhibition by a human milk oligosaccharide. Virology (2017)

Release Date

2017-05-24

Peptides

Capsid protein VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein VP1