SMTL ID : 6is5.1

P domain of GII.3-TV24 with A-tetrasaccharide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GAL- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-FUC-A2G.1: 13 residues within 4Å: Chain A: K.147, G.185, V.186, D.187, S.233, G.234, G.235, R.236 Chain B: T.140, T.141, R.142, H.144, D.170 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.147, A:S.233, B:T.141, B:R.142, B:D.170, A:G.235, A:R.236, A:R.236 Water bridges: A:S.233, A:S.233, A:G.234, B:H.144 Hydrophobic interactions: B:T.140 Salt bridges: A:R.236 GLC-GAL-FUC-A2G.2: 13 residues within 4Å: Chain A: T.140, T.141, R.142, H.144, D.170 Chain B: K.147, G.185, V.186, D.187, S.233, G.234, G.235, R.236 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.147, B:S.233, B:G.235, A:T.141, A:R.142, A:D.170, B:R.236, B:R.236 Water bridges: A:H.144, A:H.144 Hydrophobic interactions: A:T.140 Salt bridges: B:R.236 GLC-GAL-FUC-A2G.3: 13 residues within 4Å: Chain C: T.140, T.141, R.142, H.144, D.170 Chain D: K.147, G.185, V.186, D.187, S.233, G.234, G.235, R.236 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.147, D:S.233, C:T.141, C:R.142, C:D.170, D:G.235, D:R.236, D:R.236 Water bridges: D:S.233, D:S.233, C:H.144, C:H.144, C:T.140, C:D.172 Hydrophobic interactions: C:T.140 Salt bridges: D:R.236 GLC-GAL-FUC-A2G.4: 13 residues within 4Å: Chain C: K.147, G.185, V.186, D.187, S.233, G.234, G.235, R.236 Chain D: T.140, T.141, R.142, H.144, D.170 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:K.147, C:S.233, C:G.235, D:T.141, D:R.142, D:R.142, D:D.170, C:R.236, C:R.236 Water bridges: C:S.233, C:S.233, C:G.234, D:H.144, D:H.144, C:D.187 Hydrophobic interactions: D:T.140 Salt bridges: C:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Structural basis of host ligand specificity change of GII porcine noroviruses from their closely related GII human noroviruses. Emerg Microbes Infect (2019)

Release Date

2019-11-20

Peptides

VP1 Capsid protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

VP1 Capsid protein

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