SMTL ID : 4x7e.1

Crystal structure of norovirus GII.10 P domain in complex with Nano-85

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-oligomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Q.54, N.86, L.87, N.88, L.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.87, A:N.88, A:N.88 EDO.2: 7 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, L.87, K.170 Chain C: P.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.58 EDO.3: 6 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, V.98, L.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:G.51 EDO.4: 4 residues within 4Å: Chain A: Y.142, T.189, L.190, S.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.192, A:S.192, A:S.192 EDO.6: 8 residues within 4Å: Chain A: P.22 Chain C: L.56, T.58, G.59, A.62, R.64, L.87, K.170 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.58, C:R.64 EDO.7: 5 residues within 4Å: Chain C: Q.54, N.86, L.87, N.88, L.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.87, C:N.88, C:N.88

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: P.20, P.57, T.58 Chain C: P.20, P.57, T.58 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.20, C:T.58 Water bridges: A:P.57, A:I.60 ACT.8: 3 residues within 4Å: Chain C: D.46, G.47, S.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.250 ACT.9: 5 residues within 4Å: Chain C: R.261 Chain D: S.30, I.31, S.53, G.54 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.31 Salt bridges: C:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., Nanobody binding to a conserved epitope promotes norovirus particle disassembly. J.Virol. (2015)

Release Date

2014-12-31

Peptides

Capsid protein: AC
Nano-85 Nanobody: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

Capsid protein

Nano-85 Nanobody

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