SMTL ID : 6h6y.1 (1 other biounit)

GI.1 human norovirus protruding domain in complex with Nano-7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-2-2-mer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: F.126, V.127, N.168, Y.169, G.170, S.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.168 NA.3: 5 residues within 4Å: Chain B: F.126, V.127, N.168, G.170, S.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.126 NA.4: 4 residues within 4Å: Chain B: S.30, P.31, D.32, V.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.30, B:V.34 Water bridges: B:S.30 NA.5: 5 residues within 4Å: Chain B: N.74, L.75, F.83, H.84, P.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.83, B:F.83 Water bridges: B:N.74

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

EDO.2: 9 residues within 4Å: Chain A: H.60, K.63, R.65, L.78, D.79, F.109, V.144 Chain B: L.22, P.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.63, A:R.65

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: P.55, V.56, I.92 Chain B: S.14 Chain C: R.100, L.101 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: S.14 Chain B: P.55, V.56, I.92 Chain D: R.100, L.101 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruoff, K. et al., Structural Basis of Nanobodies Targeting the Prototype Norovirus. J. Virol. (2019)

Release Date

2018-12-19

Peptides

Capsid protein VP1: AB
Nanobody (VHH) Nano-7: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Capsid protein VP1

Nanobody (VHH) Nano-7

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