SMTL ID : 6xw5.1

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5820

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Y.68, V.112, T.114, K.124, T.126, L.159, V.160, V.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.126 Water bridges: A:T.114, A:V.160 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:R.204, A:R.206, A:D.223 EDO.4: 6 residues within 4Å: Chain A: E.229, S.232, W.233 Chain B: S.232, W.233, S.236 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.232, A:E.229 Water bridges: A:S.232, A:S.236 EDO.5: 8 residues within 4Å: Chain A: Q.113, T.116, R.165 Chain B: A.20, P.21, Y.23, Y.208, R.210 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.23, B:Y.23, B:R.210, A:Q.113 Water bridges: B:Y.208 EDO.6: 8 residues within 4Å: Chain B: R.17, L.31, D.176, R.204, R.206, A.221, I.222, D.223 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.17, B:D.176, B:D.176, B:R.204, B:R.206, B:D.223 EDO.7: 7 residues within 4Å: Chain A: L.12 Chain B: P.53, I.54, S.55, W.58, L.99 Chain D: G.101 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:I.54, B:S.55, B:W.58, D:G.101 EDO.8: 4 residues within 4Å: Chain A: L.31, R.206, A.221 Chain B: T.119 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.28, A:D.28, B:T.119, B:T.119 EDO.9: 6 residues within 4Å: Chain C: S.70, R.71, D.72, M.77, V.78, S.79 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.70, C:M.77 Water bridges: C:R.19 EDO.10: 3 residues within 4Å: Chain C: A.55, Y.56, T.57 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.55, C:T.57, C:T.57 Water bridges: C:T.57

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 8 residues within 4Å: Chain A: Y.68, K.69, F.70, E.76, S.156, L.157, D.158, L.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.68, A:F.70, A:L.157, A:L.159

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-5820: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein

Nanobody NB-5820

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