SMTL ID : 6tsd.1

Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.145 Hydrogen bonds: A:Y.145, A:S.147 Water bridges: A:S.147, A:S.147, A:S.147, A:N.148

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

HEZ.2: 1 residues within 4Å: Ligands: HEZ.3 No protein-ligand interaction detected (PLIP) HEZ.3: 4 residues within 4Å: Chain A: Y.189, G.190, S.191 Ligands: HEZ.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.191 HEZ.12: 11 residues within 4Å: Chain A: A.204, S.208, Y.211, I.236, N.237 Chain B: N.213, S.214, L.215, D.218, H.223 Ligands: CL.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.236, B:L.215 Hydrogen bonds: A:N.237, B:H.223 Water bridges: A:A.204 HEZ.13: 5 residues within 4Å: Chain A: Y.230, V.234, T.235, E.284 Chain B: T.140 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.230, A:Y.230, A:V.234 Hydrogen bonds: A:E.284 Water bridges: A:Y.230, B:T.140

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

CL.4: 4 residues within 4Å: Chain A: G.202, I.203, F.239 Ligands: HEZ.12 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: N.248, E.249 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.245 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: V.299, E.300, T.304 Chain C: K.92 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: G.151, E.152 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: F.19, Q.20 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: T.59, G.60 Ligand excluded by PLIP

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

NA.5: 4 residues within 4Å: Chain A: T.26, A.27, S.29, N.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.26, A:S.29, A:N.68

5 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.7: 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.4, H2O.8 CA.8: 4 residues within 4Å: Chain A: N.94, W.172, V.246, N.248 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.246, A:N.248, H2O.1, H2O.2 CA.14: 1 residues within 4Å: Chain B: E.55 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.55 CA.18: 1 residues within 4Å: Chain C: T.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections. Acs Chem.Biol. (2020)

Release Date

2021-07-07

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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