SMTL ID : 8y6d.1

Norovirus GII.10 P domain and 2'-FL (tablet)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

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

GLC-GAL-FUC.1: 10 residues within 4Å: Chain A: A.131, N.132, R.133, D.162 Chain B: S.178, D.180, G.227, G.228, Y.229 Ligands: EDO.11 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.229 Hydrogen bonds: B:G.228, A:N.132, A:R.133, A:R.133, A:D.162, B:S.178, B:S.178, B:D.180, B:D.180 Water bridges: B:V.179, B:Y.229, B:Y.229

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

EDO.2: 8 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, F.63, L.87, K.170 Chain B: P.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.58 EDO.3: 11 residues within 4Å: Chain A: L.6, P.7, L.9, T.10, L.14, F.219, P.239, W.242, Y.262, Y.299, F.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.9, A:W.242, A:F.300 EDO.4: 6 residues within 4Å: Chain A: Q.54, N.86, L.87, N.88, T.90, L.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.87, A:N.88, A:N.88 Water bridges: A:N.88, A:L.102 EDO.5: 7 residues within 4Å: Chain A: R.76, G.77, T.78, V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 EDO.8: 7 residues within 4Å: Chain A: K.2, P.3, T.5, H.245, E.249 Chain B: E.249 Ligands: PEG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.5 Water bridges: A:P.3, A:P.3, A:E.249 EDO.9: 3 residues within 4Å: Chain B: W.305, V.306, N.307 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.307 EDO.10: 9 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, F.63, R.64, L.87, K.170 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.58, B:R.64, B:R.64 EDO.11: 6 residues within 4Å: Chain A: H.135, E.159 Chain B: E.136, W.158, K.226 Ligands: GLC-GAL-FUC.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.226 Water bridges: B:E.136, B:E.136, A:H.135, A:H.135 EDO.12: 6 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, T.90, L.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.87, B:N.88, B:N.88 Water bridges: B:N.88, B:L.102 EDO.13: 7 residues within 4Å: Chain B: R.76, G.77, T.78, V.138, S.156, T.157, W.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.156, B:S.156 Water bridges: B:R.76, B:S.156

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 2 residues within 4Å: Chain A: Y.142, H.184 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 8 residues within 4Å: Chain A: K.2, Q.248, E.249 Chain B: T.5, I.8, H.245, E.249 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.2 Water bridges: A:Q.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hansman, G. et al., Norovirus GII.10 P domain and 2'-FL (tablet). To Be Published

Release Date

2024-06-19

Peptides

GII.10 norovirus P domain in complex with 2'-FL (tablet): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GII.10 norovirus P domain in complex with 2'-FL (tablet)

Related Entries With Identical Sequence