SMTL ID : 8en6.1

Structure of GII.4 norovirus in complex with Nanobody 76

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.49, L.50, G.51, T.53, I.94, L.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:G.51, A:G.51 GOL.2: 5 residues within 4Å: Chain A: L.49, Q.54, L.55 Chain C: E.13 Ligands: GOL.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:L.55, C:E.13, C:E.13 Water bridges: A:S.56 GOL.4: 6 residues within 4Å: Chain A: Q.54, N.59, Q.83 Chain C: E.12, E.13 Ligands: GOL.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:L.55, A:S.56, A:Q.83, C:E.13, C:E.13 GOL.8: 6 residues within 4Å: Chain C: L.49, L.50, G.51, T.53, I.94, L.98 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.53 Water bridges: C:L.49, C:G.51, C:G.51, C:H.194 GOL.14: 3 residues within 4Å: Chain D: Q.13, G.16, S.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.17 Water bridges: D:Q.13

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 5 residues within 4Å: Chain A: L.263, H.282, L.284, V.285, M.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.263, A:L.284 Hydrogen bonds: A:H.282, A:V.285 IPA.15: 2 residues within 4Å: Chain D: L.11, Q.13 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.13 Hydrogen bonds: D:L.11 Water bridges: D:Q.13

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

EDO.5: 3 residues within 4Å: Chain A: E.13 Chain C: L.55, Y.239 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: E.24, T.214 Chain C: W.85, N.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.85, C:N.157 EDO.7: 4 residues within 4Å: Chain A: N.84, W.85 Chain C: E.12, E.24 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.24 EDO.9: 7 residues within 4Å: Chain C: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.212, C:D.227 Water bridges: C:Q.179, C:Q.281 EDO.11: 5 residues within 4Å: Chain C: F.27, R.174, R.212, D.225, Q.281 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.174, C:R.212, C:D.225, C:Q.281, C:Q.281 EDO.12: 4 residues within 4Å: Chain C: G.47, V.48, L.49, Y.239 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.49, C:L.49 EDO.13: 3 residues within 4Å: Chain D: R.38, E.46, F.62 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.38

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 7 residues within 4Å: Chain C: V.67, T.68, H.69, Y.76, F.152, E.153, A.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kher, G. et al., Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies. J.Virol. (2023)

Release Date

2023-03-15

Peptides

GII.4 P domain: AC
Nanobody 76: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

GII.4 P domain

Nanobody 76

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