SMTL ID : 7qb5.1

Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.1: 4 residues within 4Å: Chain A: R.143, Y.145, A.146, S.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.145, A:S.147

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.2: 5 residues within 4Å: Chain A: N.154, T.188, Y.189, G.190, S.191 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.154 Hydrogen bonds: A:S.191

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 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.5: 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.8 CA.9: 1 residues within 4Å: Chain B: E.55 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.55

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

CL.6: 2 residues within 4Å: Chain A: N.248, E.249 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.245 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: K.220, D.221 Chain B: A.269, T.270, Q.271 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: D.88, G.151, E.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Exploring divalent conjugates of 5- N -acetyl-neuraminic acid as inhibitors of coxsackievirus A24 variant (CVA24v) transduction. Rsc Adv (2022)

Release Date

2022-05-18

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

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