SMTL ID : 8en5.1 (1 other biounit)

Structure of GII.4 norovirus in complex with Nanobody 56

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.49, L.50, G.51, T.53, I.94, L.98 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: N.256, L.263, P.287 Chain C: T.102 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: S.120, T.121, R.122 Chain B: S.219, G.220 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: W.85, T.112, Q.113, N.157, K.159 Chain B: P.216 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Y.239, Q.240 Chain B: V.8 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.67, T.68, H.69, F.152, A.154 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: P.7, L.9, E.233, Q.236, Y.237 Chain B: Q.236, Q.240 Ligands: EDO.20 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: L.49, L.55, L.98 Chain B: E.13 Ligands: MES.8 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: V.67, T.68, H.69, F.152, A.154 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: L.49, L.50, G.51, T.53, I.94, L.98 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: P.216 Chain B: T.112, Q.113, T.114, N.157, K.159 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: S.219, G.220 Chain B: S.120, T.121, R.122 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: T.1, K.2, E.241, A.243 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain B: T.62, F.63, R.64, L.80, A.81, S.82, Q.83, P.97, L.98 Ligands: EDO.22 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: L.182, P.183, S.184, N.192 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: V.35, Q.37, W.180, V.181, L.182 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: Q.236, Q.240 Chain B: P.7, L.9, E.233, Q.236, Y.237 Ligands: EDO.9 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: V.8 Chain B: Y.239, Q.240, E.241 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: S.82, Q.83, Y.88, E.92, I.94, P.97, L.98 Ligands: EDO.17 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: V.285 Chain C: F.27, I.28, L.29, G.30, R.31, P.32, N.77 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain D: T.24, F.27, R.31, R.72, N.74, N.77 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain D: F.27, I.28, L.29, G.30, R.31 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain D: G.30, R.31, G.53, T.102 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 8 residues within 4Å: Chain A: S.82, Q.83, Y.88, E.92, I.94, P.97, L.98 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.83, A:Q.83, A:L.98 Water bridges: A:S.82, A:N.84 Salt bridges: A:E.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kher, G. et al., Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies. J.Virol. (2023)

Release Date

2023-03-15

Peptides

GII.4 P domain: AB
Nanobody 56: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

GII.4 P domain

Nanobody 56

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