SMTL ID : 4q4y.4 (4 other biounits)

Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.145, A:S.147 Water bridges: A:S.147, A:S.147

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

HEZ.2: 3 residues within 4Å: Chain A: N.154, Y.189, S.191 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.154 Hydrogen bonds: A:S.191 HEZ.3: 4 residues within 4Å: Chain A: Y.230, T.235, E.284 Chain B: T.140 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:T.140, A:Y.230 Hydrophobic interactions: A:Y.230 Hydrogen bonds: A:E.284

5 x CA: CALCIUM ION(Non-covalent)

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.6, H2O.6 CA.6: 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.11: 1 residues within 4Å: Chain B: E.55 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.55, H2O.16, H2O.20 CA.14: 1 residues within 4Å: Chain C: T.4 No protein-ligand interaction detected (PLIP)

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

CL.7: 2 residues within 4Å: Chain A: N.248, E.249 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.245 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: V.299, E.300, T.304 Chain C: K.92 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: K.220, D.221 Chain B: A.269, T.270, Q.271 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: K.87, G.151, E.152 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: T.59, G.60 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: F.19, Q.20 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 1 residues within 4Å: Chain B: E.152 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.152, H2O.15, H2O.17, H2O.18, H2O.20

1 x MYR: MYRISTIC ACID(Covalent)

MYR.17: 2 residues within 4Å: Chain D: G.2, A.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zocher, G. et al., A sialic Acid binding site in a human picornavirus. Plos Pathog. (2014)

Release Date

2014-11-05

Peptides

Coxsackievirus capsid protein VP1: A
Coxsackievirus capsid protein VP2: B
Coxsackievirus capsid protein VP3: C
Coxsackievirus capsid protein VP4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

Coxsackievirus capsid protein VP1

Coxsackievirus capsid protein VP2

Coxsackievirus capsid protein VP3

Coxsackievirus capsid protein VP4

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