SMTL ID : 8y6c.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

3 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.16 12 PLIP interactions: 7 interactions with chain B, 5 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:D.180, B:D.180, B:G.228 Water bridges: A:D.162, B:A.177, B:V.179, B:Y.229 GLC-GAL-FUC.2: 10 residues within 4Å: Chain A: S.178, D.180, G.227, G.228, Y.229 Chain B: A.131, N.132, R.133, D.162 Ligands: EDO.17 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.131, A:Y.229 Hydrogen bonds: B:N.132, B:R.133, B:R.133, B:D.162, A:G.228, B:D.162, A:S.178, A:D.180, A:D.180 Water bridges: B:D.162, B:D.162, B:D.162, A:V.179, A:Y.229 GLC-GAL-FUC.3: 7 residues within 4Å: Chain A: Q.69, Q.70, V.71, Q.72, N.81, K.145, N.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.145, A:Q.69, A:Q.72, A:Q.72, A:Q.69 Water bridges: A:Q.72, A:Q.72, A:N.152, A:N.152

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

EDO.4: 8 residues within 4Å: Chain A: L.49, Q.50, G.51, T.52, T.53, Q.54, V.98, L.102 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.2, Q.248, E.249 Chain B: I.8 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: W.305, V.306, N.307, Y.310 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: R.76, G.77, T.78, V.138, S.156, T.157, W.158 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Q.54, N.86, L.87, N.88, L.102 Ligands: EDO.20 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: L.190, P.191, S.192, T.198, L.199, N.200 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, F.63, R.64, L.87, K.170 Chain B: P.22 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: T.83, V.84, T.85, N.86, T.90, P.91, F.92 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: A.134, H.135, E.136, W.158, E.159 Chain B: E.136, K.226 Ligands: EDO.16, PEG.27 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: V.25, Y.27, R.220, F.222, G.290, P.291 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: G.47, E.48, L.49, Q.50, Y.247 Ligands: EDO.23 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: H.135 Chain B: E.136, W.158, K.226 Ligands: GLC-GAL-FUC.1, EDO.13, PEG.27 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: H.135, E.159, D.162 Ligands: GLC-GAL-FUC.2, GLC-GAL-FUC.2, PEG.27 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: R.76, G.77, V.138, S.156, T.157, W.158 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: N.88 Chain B: T.10, G.12, E.13, T.296, N.297 Ligands: EDO.8 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: T.68, N.81, T.83, N.152 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain B: D.73, H.75, H.79, V.138, I.139, A.140, S.143, Q.154, F.155, S.156 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain B: L.49, Q.50, G.51, T.52, T.53, Q.54, V.98, L.102 Ligands: EDO.15 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: Q.244, H.245, Q.248 Chain B: P.7, L.9, E.241, Q.244, H.245 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: V.179, D.180, A.181, S.183, H.184, F.185 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: D.46, G.47, E.48, S.250 Ligand excluded by PLIP

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

PEG.10: 6 residues within 4Å: Chain A: A.34, I.35, Q.37, W.188, T.189, L.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.35, A:Q.37 Water bridges: A:Q.37, A:L.190 PEG.27: 10 residues within 4Å: Chain A: E.136, K.226 Chain B: A.134, H.135, E.136, W.158, E.159 Ligands: EDO.13, EDO.16, EDO.17 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.135, B:E.136, B:E.159, A:K.226 Water bridges: B:W.158, B:E.159, B:T.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-06-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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