SMTL ID : 6h6z.1

GI.1 human norovirus protruding domain in complex with Nano-62

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-mer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: P.123, F.126, N.168, G.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.170 NA.7: 4 residues within 4Å: Chain B: P.123, F.126, N.168, G.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.170

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

EDO.2: 4 residues within 4Å: Chain A: L.232, H.234, E.246, Y.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.246 Water bridges: A:N.243 EDO.3: 6 residues within 4Å: Chain A: V.161, D.162, L.163, W.164, Y.205, N.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.163, A:W.164, A:A.204, A:N.206 EDO.4: 7 residues within 4Å: Chain A: A.20, P.21, L.22, L.147, S.148, M.199, P.200 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:P.21, B:K.63 EDO.5: 5 residues within 4Å: Chain A: P.55, V.56, S.57, H.60 Chain B: S.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.14, A:V.56, A:S.57 EDO.6: 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 EDO.8: 6 residues within 4Å: Chain B: Q.116, Y.117, D.118, N.136, G.137, I.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.118, B:D.118, B:N.136 EDO.9: 6 residues within 4Å: Chain B: A.20, P.21, L.22, L.147, S.148, M.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.148

Links

RCSB   PDBe   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

Related Entries With Identical Sequence