SMTL ID : 6t48.1

Bovine enterovirus F3 in complex with glutathione and a Cysteinylglycine dipeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 5 residues within 4Å: Chain A: M.247, T.248, P.249 Chain C: D.235 Ligands: GLY.12 3 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: C:R.233 Water bridges: G.12, A:M.247

1 x STE: STEARIC ACID(Non-covalent)

STE.2: 15 residues within 4Å: Chain A: I.90, N.91, F.92, F.114, V.136, P.160, S.161, V.162, V.173, V.175, Y.184, F.186, N.208, L.213 Chain C: M.24 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.92, A:F.114, A:V.162, A:Y.184, A:F.186 Hydrogen bonds: A:N.91, A:F.92, A:N.208

1 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 6 residues within 4Å: Chain A: L.75, M.78, R.229 Chain C: Q.238, E.239, G.240 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:R.229, A:R.229, C:E.239 Salt bridges: A:R.229 Hydrogen bonds: C:E.239

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: S.198, G.199, S.200 Chain B: S.135 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.135, B:S.135, A:S.200, A:S.200 Water bridges: A:G.199, A:G.199 SO4.5: 2 residues within 4Å: Chain A: R.87, Y.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.89 Water bridges: A:R.87, A:R.87, A:R.87 Salt bridges: A:R.87 SO4.10: 3 residues within 4Å: Chain B: S.132, A.133, E.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.134 Water bridges: B:S.135 SO4.13: 2 residues within 4Å: Chain C: A.65, R.68 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.65 Salt bridges: C:R.68 SO4.14: 4 residues within 4Å: Chain C: L.180, E.181, N.182, T.183 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.181, C:N.182, C:T.183 Water bridges: C:R.188, C:R.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: D.260, T.261, T.262, K.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.260, A:T.262 GOL.7: 8 residues within 4Å: Chain A: F.186, S.187, R.243, S.244 Chain B: K.129, D.158, T.160, Y.168 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.129, B:Y.168, A:F.186, A:R.243, A:S.244 Water bridges: B:Q.131, B:D.158, A:S.187

4 x K: POTASSIUM ION(Non-covalent)

K.8: 6 residues within 4Å: Chain A: T.30, P.31, L.33, Q.34 Chain D: E.63, A.65 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:L.33, D:A.65 K.9: 4 residues within 4Å: Chain A: T.14, V.15, N.17, N.57 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.15 K.11: 1 residues within 4Å: Chain B: Q.53 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain A: T.41, S.42 Chain C: D.114, Q.222 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.42

1 x GLY: GLYCINE(Non-covalent)

GLY.12: 6 residues within 4Å: Chain A: M.247, F.264 Chain C: Q.95, S.96, D.235 Ligands: CYS.1 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: C:Q.95, A:F.264, G.12 Water bridges: C:Q.95, C:R.233, C:R.233, C.1

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 3 residues within 4Å: Chain C: I.90, T.179, L.180 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duyvesteyn, H.M.E. et al., Glutathione facilitates enterovirus assembly by binding at a druggable pocket. Commun Biol (2020)

Release Date

2020-01-15

Peptides

VP1: A
VP2: B
VP3: C
VP4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

VP1

VP2

VP3

VP4

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