SMTL ID : 6xw7.1 (1 other biounit)

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829 and glycochenodeoxycholate (GCDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Y.71, Q.116, T.117, E.118, V.163, G.165, R.166, V.167 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.71, A:Y.71, A:E.118 Water bridges: A:Q.116, A:E.118, A:E.118 EDO.2: 5 residues within 4Å: Chain A: N.37, P.195, I.196, G.197, P.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37 Water bridges: A:F.199 EDO.6: 8 residues within 4Å: Chain A: T.50, L.51, L.52 Chain C: S.50, I.51, S.57, N.59, R.99 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.57, C:N.59, C:R.99, A:L.51 Water bridges: C:N.59, C:R.99, A:G.53 EDO.7: 8 residues within 4Å: Chain B: T.50, L.51, L.52 Chain D: S.50, I.51, S.57, N.59, R.99 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:L.51, D:S.57, D:N.59, D:R.99 Water bridges: B:G.53

2 x CHO: GLYCOCHENODEOXYCHOLIC ACID(Non-covalent)

CHO.3: 15 residues within 4Å: Chain A: W.21, A.23, Y.26, Y.211, M.212, R.213 Chain B: A.66, E.68, I.86, Q.88, G.90, Q.116, R.166, V.167, R.168 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:I.86, B:R.166, A:Y.26, A:Y.211 Hydrogen bonds: B:E.68, B:E.68, B:R.166, A:Y.211, A:Y.211, A:R.213 Water bridges: B:R.168, A:R.213, A:R.213, A:R.213, A:R.213 Salt bridges: B:R.168, A:R.213 CHO.4: 15 residues within 4Å: Chain A: A.66, I.86, Q.88, G.90, Q.116, R.166, V.167, R.168 Chain B: W.21, P.22, A.23, Y.26, Y.211, M.212, R.213 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.26, B:Y.26, B:Y.211, A:I.86, A:R.166, A:R.168 Hydrogen bonds: B:Y.211, B:Y.211, B:R.213, A:R.166 Water bridges: B:R.213, B:R.213, A:R.168, A:R.168 Salt bridges: B:R.213, A:R.168

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: Q.214, D.216, E.223 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.216, B:E.223, H2O.9, H2O.15, H2O.15

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-5829: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein

Nanobody NB-5829

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