SMTL ID : 5o03.1

GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-32

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-2-2-mer

Ligands

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: Y.247, Q.248, S.250 Chain B: I.8 No protein-ligand interaction detected (PLIP) IMD.10: 4 residues within 4Å: Chain A: I.8 Chain B: Y.247, Q.248, S.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.250

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

EDO.2: 6 residues within 4Å: Chain A: L.56, T.58, G.59, L.87, K.170 Chain B: P.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58 Water bridges: A:T.58, A:K.170 EDO.3: 6 residues within 4Å: Chain A: F.222, I.223, P.224 Chain B: R.118, K.170 Chain C: Q.1 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:Q.1, B:R.118, A:F.222 Water bridges: C:Q.1, B:R.118, A:N.231 EDO.4: 6 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, L.102 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.51 EDO.5: 6 residues within 4Å: Chain A: P.7, L.9, E.241, H.245 Chain B: Q.244, Q.248 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.245 Water bridges: B:Q.244 EDO.6: 4 residues within 4Å: Chain A: Q.54, L.87, N.88, L.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.54, A:L.87, A:N.88, A:N.88 Water bridges: A:L.55 EDO.7: 4 residues within 4Å: Chain A: E.136, W.158, K.226 Chain B: H.135 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.135, A:K.226 EDO.8: 6 residues within 4Å: Chain A: R.76, G.77, V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 EDO.9: 2 residues within 4Å: Chain A: T.95, D.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.95, A:D.97, A:D.97 EDO.11: 7 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, L.87, K.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.58 EDO.12: 6 residues within 4Å: Chain B: R.76, G.77, V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.157 EDO.13: 6 residues within 4Å: Chain A: Q.244, Q.248 Chain B: P.7, L.9, E.241, H.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.245 EDO.14: 7 residues within 4Å: Chain B: P.94, T.95, E.96, D.97, K.149, M.201, N.202 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.97, B:D.97, B:K.149, B:K.149, B:N.202 EDO.15: 5 residues within 4Å: Chain A: L.55, L.102, Y.247 Chain B: E.13 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.13 EDO.16: 3 residues within 4Å: Chain B: E.136, W.158, K.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.226 EDO.17: 5 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.88, B:N.88 Water bridges: B:L.87, B:L.87

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-32: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein

Nanobody (VHH) Nano-32

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