SMTL ID : 5o04.1

GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-26 and Nano-85

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: S.116, Q.117, R.118, N.132, P.168 Chain B: P.224, L.225 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, R.64, K.170 Chain B: P.22 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: F.185, Q.187, N.231, P.232, A.233 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: L.190, N.200 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.76, V.138, S.156, W.158 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Y.27, R.220, F.222, P.291 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: F.222, I.223, P.224 Chain B: R.118, K.170 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: T.5, L.6, I.8, R.301, F.302 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: T.141, Y.142, S.143, P.144, F.146, P.191, S.192, G.195 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, L.87, K.170 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: H.135 Chain B: E.136, W.158, K.226 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: R.76, V.138, S.156, T.157, W.158 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain C: V.34, G.35, Y.37, Q.50, N.96, R.98 Ligand excluded by PLIP EDO.16: 10 residues within 4Å: Chain F: Y.32, M.34, G.71, D.72, N.73, N.76, T.77, V.78, R.97 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain F: Y.32, I.51, S.52, S.53, G.55, G.71, N.73 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain F: F.29, D.99, S.101, A.104, P.105, S.107 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization. PLoS Pathog. (2017)

Release Date

2017-10-04

Peptides

Capsid protein: AB
Nanobody (VHH) Nano-26: CE
Nanobody (VHH) Nano-85: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

E
F

D
D

F
C

Capsid protein

Nanobody (VHH) Nano-26

Nanobody (VHH) Nano-85

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