SMTL ID : 5o02.1

GII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.52, Q.53, G.54, T.56, V.98, L.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.56 Water bridges: A:G.54 EDO.2: 3 residues within 4Å: Chain A: P.10, E.234, H.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.238 EDO.3: 4 residues within 4Å: Chain A: L.264, Y.283, L.285, M.308 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.283 EDO.4: 1 residues within 4Å: Chain A: E.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.16, A:E.16 EDO.5: 4 residues within 4Å: Chain B: R.45, Y.95, W.114 Ligands: IMD.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.45, B:R.45 Water bridges: B:Y.95 EDO.6: 4 residues within 4Å: Chain B: A.40, P.41, V.93, Q.119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.40, B:Q.119

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 3 residues within 4Å: Chain B: R.45, W.114 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.45

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: A
Nanobody (VHH) Nano-4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Capsid protein

Nanobody (VHH) Nano-4

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