SMTL ID : 8emy.1

Structure of GII.4 norovirus in complex with Nanobody 82

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-6-6-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: T.44, D.46, K.270, S.271 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: L.263, F.264, H.282, D.283, L.284, V.285, M.307 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.106, T.127, Y.129, E.145, I.166 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: S.120, T.121, R.122 Chain D: S.219, G.220, Y.221 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: T.77, R.141 Chain G: D.56, I.57, T.58 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: H.69, T.71, G.72 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain B: F.27, F.34, Q.179, W.180, F.210, R.212, D.227, Q.281 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: T.91, E.92, E.93 Chain J: K.97, D.104 Ligands: EDO.11 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: S.120, T.121, R.122 Chain E: S.219, G.220, Y.221 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: D.89, T.91 Chain J: V.37, P.45, E.46, W.47, K.97 Ligands: EDO.9 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain C: L.263, H.282, V.285, M.307 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain C: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: S.82, Y.88, E.92, I.94, P.97, L.98 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain C: E.93, H.194 Chain H: N.102 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain C: S.120, T.121, R.122 Chain F: S.219, G.220, Y.221 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: D.89, T.91 Chain H: V.37, P.45, E.46, W.47 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain D: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain D: D.66, N.79, L.80, A.81, W.85, N.86, D.87 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: P.216 Chain D: T.112, Q.113, N.157, K.159 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain D: E.24, K.25, I.286 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: T.117, D.118 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: E.153, A.154, N.155, Q.156 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain D: S.82, N.84, N.86, D.87 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain E: L.49, L.50, G.51, T.53, I.94, L.98 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain B: P.216 Chain E: W.85, T.112, Q.113, T.114, N.157, T.158, K.159 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain E: F.27, G.29, P.30, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain E: T.115, T.117, D.118, S.120, R.122, E.153 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain E: D.89, T.91 Chain L: V.37, P.45, E.46, W.47 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain F: G.65, D.66, A.81, W.85, R.116, N.155, Q.156, N.157 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain F: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain F: T.91, E.92, E.93 Chain I: K.97, D.104 Ligands: EDO.34 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: T.117 Chain F: R.174 Chain J: G.26, F.27, T.28 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain F: D.89, T.91 Chain I: V.37, P.45, E.46, W.47 Ligands: EDO.32 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain K: Y.95, R.106, G.107, Q.108 Ligand excluded by PLIP

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: ABCDEF
Nanobody 82: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

GII.4 P domain

Nanobody 82

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