SMTL ID : 5omm.1

GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-14

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-oligomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: P.7, E.241, H.245 Chain B: Q.244, Q.248 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: S.192, A.196, T.198, L.199 Ligands: EDO.9 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: S.164, S.165 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: P.20, P.57, T.58 Chain B: P.20, P.57, T.58 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.118, K.170 Chain B: F.222, I.223, P.224 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: Y.247 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, L.102 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Q.54, N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: T.189, L.190, S.192, N.200 Ligands: EDO.2 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, L.87, K.170 Chain B: P.22 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: R.286, V.292, V.293, M.315 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: I.139, A.140, S.143, K.145, F.146, I.153, Q.154 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: A.131, N.132 Chain B: G.227, G.228, Y.229 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Q.244, Q.248 Chain B: P.7, E.241, H.245 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: L.259, D.303, S.304, V.306, Y.310 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: E.13 Chain B: L.49, Q.54, L.55 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, L.87, K.170 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: L.49, Q.50, G.51, T.53, L.102 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: A.177, S.178, D.180, G.227, G.228 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: G.77, V.138, S.156, T.157, W.158 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: Y.247, Q.248, S.250 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: Y.27, R.220, F.222, P.291 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: F.309, Y.310 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: T.78, T.160 Chain C: S.30, H.32, I.99 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization. PLoS Pathog. (2017)

Release Date

2017-10-04

Peptides

Capsid protein: AB
Nanobody (VHH) Nano-14: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Capsid protein

Nanobody (VHH) Nano-14

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