SMTL ID : 6h72.1

GI.1 human norovirus protruding domain in complex with Nano-94 and 2-fucosyllactose (2FL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLC- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-FUC.1: 9 residues within 4Å: Chain A: D.101, H.103, Q.116, D.118, W.149, S.151, P.152, S.154 Chain B: S.112 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.103, A:Q.116, A:D.118, A:D.101, A:S.151, A:S.151 Water bridges: A:Q.116, A:D.118, A:D.118, B:S.113, B:S.112 GLC-GAL-FUC.2: 8 residues within 4Å: Chain B: D.101, H.103, Q.116, D.118, W.149, S.151, P.152, S.154 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.116, B:D.118, B:S.151, B:S.151 Water bridges: B:Q.116, A:S.113

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

EDO.3: 7 residues within 4Å: Chain A: A.20, P.21, L.22, L.147, S.148, M.199, P.200 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain B: A.20, P.21, L.22, L.147, S.148, M.199, P.200 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.148, B:S.148

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-94: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein VP1

Nanobody (VHH) Nano-94

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