SMTL ID : 4x7f.1

Crystal structure of norovirus GII.10 P domain in complex with Nano-25

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: T.44, D.46, R.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.46, A:R.278

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

EDO.2: 4 residues within 4Å: Chain A: N.86, L.87, N.88, L.102 Ligand excluded by PLIP EDO.3: 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.4: 5 residues within 4Å: Chain A: F.185, Q.187, R.220, P.232, A.233 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: 6 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, V.98, L.102 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: Q.54, L.55 Chain B: E.13 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.138, S.156, T.157, W.158 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: T.10, G.12, E.13 Chain B: N.88 Ligands: EDO.20 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.22, D.24, F.222 Chain B: R.64 Ligands: EDO.19 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: Y.247, Q.248 Chain B: I.8 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.13 Chain B: L.49, Q.54, L.55 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: L.271, F.272, R.286, V.292, V.293 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.64, L.87, N.88 Chain B: P.22, I.23, D.24 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: F.185, Q.187, R.220, P.232, A.233 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.11, V.25, L.26, V.292, A.294, T.296 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: L.49, Q.50, G.51, T.53, V.98, L.102 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: F.222, I.223, P.224 Chain B: R.118, K.170 Ligands: EDO.10 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 Ligands: EDO.9 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: Y.247, Q.248, S.250 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: P.94, T.95, E.96, D.97, K.149, N.202 Ligand excluded by PLIP EDO.23: 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.25: 5 residues within 4Å: Chain A: F.211, P.212, F.309 Chain C: E.46, L.47 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: R.38, E.46, L.47, A.60, S.62 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 5 residues within 4Å: Chain A: H.135, E.136, E.159 Chain B: E.136, K.226 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.136, B:E.136, A:E.136, A:E.159 Water bridges: B:K.226 Salt bridges: B:K.226, A:H.135

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.24: 6 residues within 4Å: Chain A: P.20, P.57, T.58 Chain B: P.20, P.57, T.58 No protein-ligand interaction detected (PLIP) IMD.26: 6 residues within 4Å: Chain A: D.256, Q.308 Chain C: T.52, S.56, T.57, D.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.256 Water bridges: A:D.256

Links

RCSB   PDBe   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: AB
Nano-25 Nanobody: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Capsid protein

Nano-25 Nanobody

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