SMTL ID : 6h70.1

GI.1 human norovirus protruding domain in complex with Nano-62 and 2-fucosyllactose (2FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 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: 8 residues within 4Å: Chain A: D.101, H.103, Q.116, D.118, W.149, S.151, P.152, S.154 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.103, A:Q.116, A:D.118, A:S.151, A:S.151 Water bridges: A:Q.116, A:D.118, A:S.151, B:S.113, A:S.154, A:S.154, B:S.112 GLC-GAL-FUC.2: 9 residues within 4Å: Chain A: S.112 Chain B: D.101, H.103, Q.116, D.118, W.149, S.151, P.152, S.154 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.116, B:D.118, B:D.101, B:S.151, B:S.151 Water bridges: B:D.101, B:Q.116, B:S.151, A:S.113, B:D.101, B:S.154, A:S.112

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

NA.3: 4 residues within 4Å: Chain A: F.126, N.168, Y.169, G.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.168 NA.6: 3 residues within 4Å: Chain B: F.126, N.168, G.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.170

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

EDO.4: 5 residues within 4Å: Chain A: P.55, V.56, S.57, H.60 Chain B: S.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.56, A:S.57, A:H.60 EDO.5: 7 residues within 4Å: Chain A: A.20, P.21, L.22, L.147, S.148, M.199, P.200 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:K.63, B:K.63, B:K.63, A:P.21 EDO.7: 7 residues within 4Å: Chain B: A.20, P.21, L.22, L.147, S.148, M.199, P.200 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.63, A:K.63, A:K.63, A:K.63 EDO.8: 5 residues within 4Å: Chain A: S.14 Chain B: P.55, V.56, S.57, H.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.56, B:S.57, B:H.60

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-62: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein VP1

Nanobody (VHH) Nano-62

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