SMTL ID : 6xw4.1

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5867

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: S.105, G.133, P.134, T.135, I.178, P.179, E.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.105, A:T.135, A:P.179 EDO.2: 7 residues within 4Å: Chain A: R.17, L.31, D.176, R.206, A.221, I.222, D.223 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:D.176, A:D.176, A:R.206, A:D.223 EDO.3: 8 residues within 4Å: Chain A: Y.68, Q.113, T.114, E.115, V.160, G.162, R.163, V.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.68 EDO.4: 2 residues within 4Å: Chain A: Y.298, Q.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.298, A:Q.299 EDO.5: 7 residues within 4Å: Chain A: P.19, S.57, R.165, V.167 Chain B: P.19 Ligands: EDO.6, EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.57, A:R.165, A:R.165 EDO.6: 10 residues within 4Å: Chain A: E.111, V.167, P.168, R.210 Chain B: E.111, V.167, P.168, R.210 Ligands: EDO.5, EDO.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.168, A:R.210, B:P.168, B:R.210 EDO.7: 5 residues within 4Å: Chain A: P.19 Chain B: S.57, R.165 Ligands: EDO.5, EDO.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.57, B:R.165, B:R.165 Water bridges: A:R.210 EDO.8: 8 residues within 4Å: Chain B: Y.68, Q.113, T.114, E.115, V.160, G.162, R.163, V.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.68 Water bridges: B:E.115 EDO.9: 7 residues within 4Å: Chain B: L.31, F.174, D.176, R.206, A.221, I.222, D.223 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.17, B:D.176, B:D.176, B:R.206, B:D.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., Nanobody-Mediated Neutralization Reveals an Achilles Heel for Norovirus. J.Virol. (2020)

Release Date

2020-04-22

Peptides

Capsid protein: AB
Nanobody NB-5867: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein

Nanobody NB-5867

Related Entries With Identical Sequence