SMTL ID : 5bsy.1

Crystal structure of GII.10 P domain in complex with lemon juice

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: W.158 No protein-ligand interaction detected (PLIP) EDO.2: 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 Water bridges: A:R.76 EDO.5: 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:L.87, B:N.88, B:N.88 Water bridges: B:N.88 EDO.6: 8 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, R.64, L.87, K.170 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.58, B:R.64, B:R.64

1 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 9 residues within 4Å: Chain A: N.119, A.131, N.132, R.133, D.162, S.164 Chain B: G.227, G.228, Y.229 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.119, A:N.132, A:N.132, A:R.133, A:S.164, B:G.228 Salt bridges: A:R.133, A:R.133 Water bridges: B:Y.229, B:Y.229

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 5 residues within 4Å: Chain A: Q.248 Chain B: P.7, E.241, H.245, Q.248 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.245, B:Q.248, A:Q.248 NO3.7: 7 residues within 4Å: Chain B: H.79, V.138, I.139, A.140, Q.154, F.155, S.156 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.140 Water bridges: B:H.79, B:A.140, B:S.143, B:Q.154, B:S.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., Treatment of norovirus particles with citrate. Virology (2015)

Release Date

2015-09-09

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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