SMTL ID : 4q4w.3 (4 other biounits)

High-resolution crystal structure of Coxsackievirus A24v

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-oligomer

Ligands

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

HEZ.1: 7 residues within 4Å: Chain A: N.154, T.188, Y.189, G.190, S.191 Chain E: N.154, G.190 Ligand excluded by PLIP HEZ.2: 5 residues within 4Å: Chain A: T.88, I.89, D.116, T.117 Chain C: T.234 Ligand excluded by PLIP HEZ.9: 4 residues within 4Å: Chain A: Y.230, V.234, T.235 Chain B: T.140 Ligand excluded by PLIP HEZ.12: 5 residues within 4Å: Chain E: N.154, T.188, Y.189, G.190, S.191 Ligand excluded by PLIP HEZ.13: 7 residues within 4Å: Chain A: Y.175, Q.178 Chain E: T.88, I.89, D.116, T.117 Chain G: T.234 Ligand excluded by PLIP HEZ.20: 4 residues within 4Å: Chain E: Y.230, V.234, T.235 Chain F: T.140 Ligand excluded by PLIP HEZ.23: 5 residues within 4Å: Chain I: N.154, T.188, Y.189, G.190, S.191 Ligand excluded by PLIP HEZ.24: 7 residues within 4Å: Chain I: T.88, I.89, D.116, T.117 Chain K: T.234 Chain M: Y.175, Q.178 Ligand excluded by PLIP HEZ.31: 4 residues within 4Å: Chain I: Y.230, V.234, T.235 Chain J: T.140 Ligand excluded by PLIP HEZ.34: 7 residues within 4Å: Chain I: N.154, G.190 Chain M: N.154, T.188, Y.189, G.190, S.191 Ligand excluded by PLIP HEZ.35: 5 residues within 4Å: Chain M: T.88, I.89, D.116, T.117 Chain O: T.234 Ligand excluded by PLIP HEZ.42: 4 residues within 4Å: Chain M: Y.230, V.234, T.235 Chain N: T.140 Ligand excluded by PLIP HEZ.45: 7 residues within 4Å: Chain Q: N.154, T.188, Y.189, G.190, S.191 Chain U: N.154, G.190 Ligand excluded by PLIP HEZ.46: 5 residues within 4Å: Chain Q: T.88, I.89, D.116, T.117 Chain S: T.234 Ligand excluded by PLIP HEZ.53: 4 residues within 4Å: Chain Q: Y.230, V.234, T.235 Chain R: T.140 Ligand excluded by PLIP HEZ.56: 5 residues within 4Å: Chain U: N.154, T.188, Y.189, G.190, S.191 Ligand excluded by PLIP HEZ.57: 7 residues within 4Å: Chain Q: Y.175, Q.178 Chain U: T.88, I.89, D.116, T.117 Chain W: T.234 Ligand excluded by PLIP HEZ.64: 4 residues within 4Å: Chain U: Y.230, V.234, T.235 Chain V: T.140 Ligand excluded by PLIP

24 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 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.33, A:S.34, A:S.58, A:I.61, H2O.9, H2O.107 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, 3 Ligand-Water interactions Metal complexes: D:K.63, D:A.65, H2O.6, H2O.6, H2O.12 CA.10: 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.16 CA.14: 4 residues within 4Å: Chain E: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:T.26, E:A.27, E:S.29, E:N.68 CA.15: 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.41 CA.16: 4 residues within 4Å: Chain E: V.41, L.44 Chain H: K.63, A.65 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:K.63, H:A.65, H2O.37, H2O.37, H2O.43 CA.21: 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.47 CA.25: 4 residues within 4Å: Chain I: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:T.26, I:A.27, I:S.29, I:N.68 CA.26: 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.72 CA.27: 4 residues within 4Å: Chain I: V.41, L.44 Chain L: K.63, A.65 5 PLIP interactions: 2 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:K.63, L:A.65, H2O.69, H2O.69, H2O.74 CA.32: 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.79 CA.36: 4 residues within 4Å: Chain M: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:T.26, M:A.27, M:S.29, M:N.68 CA.37: 4 residues within 4Å: Chain M: T.33, S.34, S.58, I.61 6 PLIP interactions: 4 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:T.33, M:S.34, M:S.58, M:I.61, H2O.103, H2O.138 CA.38: 4 residues within 4Å: Chain M: V.41, L.44 Chain P: K.63, A.65 5 PLIP interactions: 2 interactions with chain P, 3 Ligand-Water interactions Metal complexes: P:K.63, P:A.65, H2O.100, H2O.100, H2O.106 CA.43: 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.110 CA.47: 4 residues within 4Å: Chain Q: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.26, Q:A.27, Q:S.29, Q:N.68 CA.48: 4 residues within 4Å: Chain Q: T.33, S.34, S.58, I.61 6 PLIP interactions: 4 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:T.33, Q:S.34, Q:S.58, Q:I.61, H2O.13, H2O.135 CA.49: 4 residues within 4Å: Chain Q: V.41, L.44 Chain T: K.63, A.65 5 PLIP interactions: 2 interactions with chain T, 3 Ligand-Water interactions Metal complexes: T:K.63, T:A.65, H2O.131, H2O.131, H2O.137 CA.54: 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.141 CA.58: 4 residues within 4Å: Chain U: T.26, A.27, S.29, N.68 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:T.26, U:A.27, U:S.29, U:N.68 CA.59: 4 residues within 4Å: Chain U: T.33, S.34, S.58, I.61 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:T.33, U:S.34, U:S.58, U:I.61, H2O.166 CA.60: 4 residues within 4Å: Chain U: V.41, L.44 Chain X: K.63, A.65 5 PLIP interactions: 2 interactions with chain X, 3 Ligand-Water interactions Metal complexes: X:K.63, X:A.65, H2O.163, H2O.163, H2O.168 CA.65: 1 residues within 4Å: Chain V: E.55 2 PLIP interactions: 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.55, H2O.173

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

CL.6: 4 residues within 4Å: Chain A: N.248, E.249 Chain E: T.141, K.258 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.245 Chain E: R.260 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.11: 3 residues within 4Å: Chain B: D.88, G.151, E.152 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain E: N.248, E.249 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain E: R.245 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain E: K.220, D.221 Chain F: A.269, T.270, Q.271 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain F: D.88, G.151, E.152 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain I: N.248, E.249 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain I: R.245 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain I: K.220, D.221 Chain J: A.269, T.270, Q.271 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain J: D.88, G.151, E.152 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain I: T.141, K.258 Chain M: N.248, E.249 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain I: R.260 Chain M: R.245 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain M: K.220, D.221 Chain N: A.269, T.270, Q.271 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain N: D.88, G.151, E.152 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain Q: N.248, E.249 Chain U: T.141, K.258 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain Q: R.245 Chain U: R.260 Ligand excluded by PLIP CL.52: 5 residues within 4Å: Chain Q: K.220, D.221 Chain R: A.269, T.270, Q.271 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain R: D.88, G.151, E.152 Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain U: N.248, E.249 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain U: R.245 Ligand excluded by PLIP CL.63: 5 residues within 4Å: Chain U: K.220, D.221 Chain V: A.269, T.270, Q.271 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain V: D.88, G.151, E.152 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: AEIMQU
Coxsackievirus capsid protein VP2: BFJNRV
Coxsackievirus capsid protein VP3: CGKOSW
Coxsackievirus capsid protein VP4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

U
1

B
2

F
2

J
2

N
2

R
2

V
2

C
3

G
3

K
3

O
3

S
3

W
3

D
4

H
4

L
4

P
4

T
4

X
4

Coxsackievirus capsid protein VP1

Coxsackievirus capsid protein VP2

Coxsackievirus capsid protein VP3

Coxsackievirus capsid protein VP4

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