SMTL ID : 4q4x.2 (4 other biounits)

Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-5-5-5-5-mer

Ligands

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

SIA.1: 6 residues within 4Å: Chain A: R.143, Y.145, A.146, S.147 Chain Q: Y.250, P.252 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain A Hydrophobic interactions: Q:P.252 Hydrogen bonds: A:Y.145, A:S.147 SIA.15: 6 residues within 4Å: Chain A: Y.250, P.252 Chain E: R.143, Y.145, A.146, S.147 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Y.145, E:S.147 Hydrophobic interactions: A:P.252 SIA.29: 6 residues within 4Å: Chain E: Y.250, P.252 Chain I: R.143, Y.145, A.146, S.147 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: E:P.252 Hydrogen bonds: I:Y.145, I:S.147 SIA.43: 6 residues within 4Å: Chain I: Y.250, P.252 Chain M: R.143, Y.145, A.146, S.147 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain M Hydrophobic interactions: I:P.252 Hydrogen bonds: M:Y.145, M:S.147 SIA.57: 6 residues within 4Å: Chain M: Y.250, P.252 Chain Q: R.143, Y.145, A.146, S.147 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain M Hydrogen bonds: Q:Y.145, Q:S.147 Hydrophobic interactions: M:P.252

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

HEZ.2: 6 residues within 4Å: Chain A: N.154, Y.189, G.190, S.191 Chain E: N.154, G.190 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:N.154 Hydrogen bonds: A:G.190, E:N.154 HEZ.3: 7 residues within 4Å: Chain A: Y.175, Q.178 Chain E: T.88, I.89, D.116, T.117 Chain G: T.234 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.175, A:Q.178, E:T.88, E:T.88 Water bridges: A:Q.178, E:D.116 Hydrophobic interactions: E:I.89, E:T.117 HEZ.16: 6 residues within 4Å: Chain E: N.154, Y.189, G.190, S.191 Chain I: N.154, G.190 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: E:N.154 Hydrogen bonds: E:G.190, I:N.154 HEZ.17: 7 residues within 4Å: Chain E: Y.175, Q.178 Chain I: T.88, I.89, D.116, T.117 Chain K: T.234 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain E Hydrophobic interactions: I:I.89, I:T.117 Hydrogen bonds: I:T.88, E:Y.175, E:Q.178 Water bridges: E:Q.178 HEZ.30: 6 residues within 4Å: Chain I: N.154, Y.189, G.190, S.191 Chain M: N.154, G.190 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain M Hydrophobic interactions: I:N.154 Hydrogen bonds: I:G.190, M:N.154 HEZ.31: 7 residues within 4Å: Chain I: Y.175, Q.178 Chain M: T.88, I.89, D.116, T.117 Chain O: T.234 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain M Hydrogen bonds: I:Y.175, I:Q.178, M:T.88 Water bridges: I:Q.178 Hydrophobic interactions: M:I.89, M:T.117 HEZ.44: 6 residues within 4Å: Chain M: N.154, Y.189, G.190, S.191 Chain Q: N.154, G.190 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain Q Hydrophobic interactions: M:N.154 Hydrogen bonds: M:G.190, Q:N.154 HEZ.45: 7 residues within 4Å: Chain M: Y.175, Q.178 Chain Q: T.88, I.89, D.116, T.117 Chain S: T.234 7 PLIP interactions: 3 interactions with chain M, 4 interactions with chain Q Hydrogen bonds: M:Y.175, M:Q.178, Q:T.88 Water bridges: M:Q.178, Q:D.116 Hydrophobic interactions: Q:I.89, Q:T.117 HEZ.58: 6 residues within 4Å: Chain A: N.154, G.190 Chain Q: N.154, Y.189, G.190, S.191 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain Q Hydrogen bonds: A:N.154, Q:G.190 Hydrophobic interactions: Q:N.154 HEZ.59: 7 residues within 4Å: Chain A: T.88, I.89, D.116, T.117 Chain C: T.234 Chain Q: Y.175, Q.178 8 PLIP interactions: 3 interactions with chain Q, 5 interactions with chain A Hydrogen bonds: Q:Y.175, Q:Q.178, A:T.88, A:T.88 Water bridges: Q:Q.178, A:D.116 Hydrophobic interactions: A:I.89, A:T.117

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

NA.4: 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 NA.18: 4 residues within 4Å: Chain E: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.26, E:T.26, E:S.29, E:N.68 NA.32: 4 residues within 4Å: Chain I: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:T.26, I:S.29, I:N.68, I:N.68 NA.46: 4 residues within 4Å: Chain M: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:T.26, M:T.26, M:S.29, M:N.68 NA.60: 4 residues within 4Å: Chain Q: T.26, A.27, S.29, N.68 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:A.27, Q:S.29, Q:N.68

25 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.6: 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.7: 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.6, H2O.6 CA.11: 1 residues within 4Å: Chain B: E.55 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.55, H2O.15 CA.13: 7 residues within 4Å: Chain G: T.4 Chain K: T.4 Chain O: T.4 Ligands: CA.27, CA.41, CA.55, CA.69 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.4 CA.19: 4 residues within 4Å: Chain E: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.33, E:S.34, E:S.58, E:I.61, H2O.40 CA.20: 4 residues within 4Å: Chain E: V.41, L.44 Chain H: K.63, A.65 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: H:K.63, H:A.65, E:L.44, H2O.36, H2O.36 CA.21: 4 residues within 4Å: Chain E: N.94, W.172, V.246, N.248 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:V.246, E:N.248, H2O.36, H2O.37 CA.25: 1 residues within 4Å: Chain F: E.55 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.55, H2O.46 CA.27: 7 residues within 4Å: Chain K: T.4 Chain O: T.4 Chain S: T.4 Ligands: CA.13, CA.41, CA.55, CA.69 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.4 CA.33: 4 residues within 4Å: Chain I: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:T.33, I:S.34, I:S.58, I:I.61, H2O.70 CA.34: 4 residues within 4Å: Chain I: V.41, L.44 Chain L: K.63, A.65 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: L:K.63, L:A.65, I:L.44, H2O.66, H2O.66 CA.35: 4 residues within 4Å: Chain I: N.94, W.172, V.246, N.248 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:V.246, I:N.248, H2O.67, H2O.67 CA.39: 1 residues within 4Å: Chain J: E.55 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.55, H2O.76 CA.41: 7 residues within 4Å: Chain C: T.4 Chain O: T.4 Chain S: T.4 Ligands: CA.13, CA.27, CA.55, CA.69 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.4 CA.47: 4 residues within 4Å: Chain M: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:T.33, M:S.34, M:S.58, M:I.61, H2O.100 CA.48: 4 residues within 4Å: Chain M: V.41, L.44 Chain P: K.63, A.65 5 PLIP interactions: 2 interactions with chain P, 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: P:K.63, P:A.65, M:L.44, H2O.96, H2O.97 CA.49: 4 residues within 4Å: Chain M: N.94, W.172, V.246, N.248 4 PLIP interactions: 2 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:V.246, M:N.248, H2O.97, H2O.97 CA.53: 1 residues within 4Å: Chain N: E.55 2 PLIP interactions: 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.55, H2O.106 CA.55: 7 residues within 4Å: Chain C: T.4 Chain G: T.4 Chain S: T.4 Ligands: CA.13, CA.27, CA.41, CA.69 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.4 CA.61: 4 residues within 4Å: Chain Q: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:T.33, Q:S.34, Q:S.58, Q:I.61, H2O.130 CA.62: 4 residues within 4Å: Chain Q: V.41, L.44 Chain T: K.63, A.65 5 PLIP interactions: 2 interactions with chain T, 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: T:K.63, T:A.65, Q:L.44, H2O.127, H2O.127 CA.63: 4 residues within 4Å: Chain Q: N.94, W.172, V.246, N.248 4 PLIP interactions: 2 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:V.246, Q:N.248, H2O.127, H2O.127 CA.67: 1 residues within 4Å: Chain R: E.55 2 PLIP interactions: 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.55, H2O.136 CA.69: 7 residues within 4Å: Chain C: T.4 Chain G: T.4 Chain K: T.4 Ligands: CA.13, CA.27, CA.41, CA.55 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.4

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

CL.8: 5 residues within 4Å: Chain A: N.248, E.249 Chain E: T.141, E.142, K.258 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.245 Chain E: R.260 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: V.299, E.300, T.304 Chain C: K.92 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: D.88, G.151, E.152 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: T.59, G.60 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain E: N.248, E.249 Chain I: T.141, E.142, K.258 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain E: R.245 Chain I: R.260 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain E: V.299, E.300, T.304 Chain G: K.92 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain F: D.88, G.151, E.152 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain G: T.59, G.60 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain I: N.248, E.249 Chain M: T.141, E.142, K.258 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain I: R.245 Chain M: R.260 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain I: V.299, E.300, T.304 Chain K: K.92 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain J: D.88, G.151, E.152 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain K: T.59, G.60 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain M: N.248, E.249 Chain Q: T.141, E.142, K.258 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain M: R.245 Chain Q: R.260 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain M: V.299, E.300, T.304 Chain O: K.92 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain N: D.88, G.151, E.152 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain O: T.59, G.60 Ligand excluded by PLIP CL.64: 5 residues within 4Å: Chain A: T.141, E.142, K.258 Chain Q: N.248, E.249 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain A: R.260 Chain Q: R.245 Ligand excluded by PLIP CL.66: 4 residues within 4Å: Chain Q: V.299, E.300, T.304 Chain S: K.92 Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain R: D.88, G.151, E.152 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain S: T.59, G.60 Ligand excluded by 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: AEIMQ
Coxsackievirus capsid protein VP2: BFJNR
Coxsackievirus capsid protein VP3: CGKOS
Coxsackievirus capsid protein VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

B
2

F
2

J
2

N
2

R
2

C
3

G
3

K
3

O
3

S
3

D
4

H
4

L
4

P
4

T
4

Coxsackievirus capsid protein VP1

Coxsackievirus capsid protein VP2

Coxsackievirus capsid protein VP3

Coxsackievirus capsid protein VP4

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