SMTL ID : 7oj7.1

Crystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.26, A:A.27, A:S.29, A:N.68 CA.2: 4 residues within 4Å: Chain A: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.33, A:S.34, A:S.58, A:I.61, H2O.10 CA.3: 4 residues within 4Å: Chain A: V.41, L.44 Chain D: K.63, A.65 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: D:K.63, D:A.65, A:L.44, H2O.3, H2O.9

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

CL.4: 2 residues within 4Å: Chain A: N.248, E.249 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.245 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: V.299, E.300, T.304 Chain C: K.92 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: D.88, G.151, E.152 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.220, D.221 Chain B: A.269, T.270, Q.271 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: D.67, S.68 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain C: T.4 Ligand excluded by PLIP

1 x 0H0: Carbohydrate component from a pentavalent N-acetylneuraminic acid conjugate(Non-covalent)

0H0.7: 4 residues within 4Å: Chain A: R.143, Y.145, A.146, S.147 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.145 Hydrogen bonds: A:Y.145, A:S.147 Water bridges: A:N.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Exploring the Effect of Structure-Based Scaffold Hopping on the Inhibition of Coxsackievirus A24v Transduction by Pentavalent N-Acetylneuraminic Acid Conjugates. Int J Mol Sci (2021)

Release Date

2021-10-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
111

B
222

C
333

D
444

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

Related Entries With Identical Sequence