SMTL ID : 8emz.1

Structure of GII.17 norovirus in complex with Nanobody 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: P.5, E.231, H.235 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: L.47, Q.48, G.49, T.51, L.97 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: Q.52, N.81, L.82, N.83, L.97 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Y.237, Q.238, S.240 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Q.68, F.154, Q.155, F.156 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: V.138, L.141, S.184, G.185, E.186, L.187 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: D.168, P.174, F.175, R.176, N.220 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Q.177, W.178, R.210, I.223, D.225 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: F.25, R.210, I.223, D.279 Ligands: EDO.8 Ligand excluded by PLIP EDO.10: 10 residues within 4Å: Chain A: L.7, T.8, L.9, L.12, F.209, W.232, Y.252, G.288, H.289, F.290 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: T.86 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.261, F.262, Y.280, L.282, V.283, M.305 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: G.15, G.16, S.17, N.84, S.85 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: S.17, L.18, R.19, L.82 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: Q.5, E.6, S.7, S.21, C.22, A.23 Ligand excluded by PLIP EDO.16: 10 residues within 4Å: Chain A: R.72, W.129, D.170 Chain B: W.53, E.101, G.102, A.103, Y.104, Y.105, R.114 Ligand excluded by PLIP

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.17 P domain: A
Nanobody 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GII.17 P domain

Nanobody 2