SMTL ID : 5c9a.2 (3 other biounits)

Crystal structure of empty coxsackievirus A16 particle

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 10 residues within 4Å: Chain A: D.112, L.113, M.114, F.135, Y.155, M.195, W.203, N.228, M.230, F.233 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.113, A:F.135, A:Y.155, A:Y.155, A:W.203, A:N.228, A:F.233 Hydrogen bonds: A:D.112, A:L.113 Water bridges: A:Q.224, A:N.228 SPH.10: 10 residues within 4Å: Chain D: D.112, L.113, M.114, F.135, Y.155, M.195, W.203, N.228, M.230, F.233 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.113, D:F.135, D:Y.155, D:Y.155, D:W.203, D:N.228, D:F.233 Hydrogen bonds: D:D.112, D:L.113 Water bridges: D:Q.224, D:N.228 SPH.19: 10 residues within 4Å: Chain G: D.112, L.113, M.114, F.135, Y.155, M.195, W.203, N.228, M.230, F.233 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:L.113, G:F.135, G:Y.155, G:Y.155, G:W.203, G:N.228, G:F.233 Hydrogen bonds: G:D.112, G:L.113 Water bridges: G:Q.224, G:N.228 SPH.28: 10 residues within 4Å: Chain J: D.112, L.113, M.114, F.135, Y.155, M.195, W.203, N.228, M.230, F.233 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:L.113, J:F.135, J:Y.155, J:Y.155, J:W.203, J:N.228, J:F.233 Hydrogen bonds: J:D.112, J:L.113 Water bridges: J:Q.224, J:N.228 SPH.37: 10 residues within 4Å: Chain M: D.112, L.113, M.114, F.135, Y.155, M.195, W.203, N.228, M.230, F.233 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:L.113, M:F.135, M:Y.155, M:Y.155, M:W.203, M:N.228, M:F.233 Hydrogen bonds: M:D.112, M:L.113 Water bridges: M:Q.224, M:N.228

5 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain F: K.7, P.8 Chain I: E.5 Chain L: G.1 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:P.8 K.11: 7 residues within 4Å: Chain D: Q.189 Chain F: V.20, S.21 Chain I: K.7, P.8 Chain L: E.5 Chain O: G.1 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:P.8 K.20: 7 residues within 4Å: Chain C: G.1 Chain G: Q.189 Chain I: V.20, S.21 Chain L: K.7, P.8 Chain O: E.5 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:P.8 K.29: 7 residues within 4Å: Chain C: E.5 Chain F: G.1 Chain J: Q.189 Chain L: V.20, S.21 Chain O: K.7, P.8 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:P.8 K.38: 7 residues within 4Å: Chain C: K.7, P.8 Chain F: E.5 Chain I: G.1 Chain M: Q.189 Chain O: V.20, S.21 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:P.8

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

CL.3: 2 residues within 4Å: Chain A: R.236 Chain D: R.250 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: K.256, H.257, V.258 Chain B: Q.44 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: H.231, P.232, Y.233 Chain C: M.66 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: K.138, S.139 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: T.137 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain B: N.15, K.34 Chain C: G.27 Chain D: Q.76, N.82 Chain E: R.43, Q.44 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain C: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: R.236 Chain G: R.250 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: K.256, H.257, V.258 Chain E: Q.44 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain E: H.231, P.232, Y.233 Chain F: M.66 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain E: K.138, S.139 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain E: T.137 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain E: N.15, K.34 Chain F: G.27 Chain G: Q.76, N.82 Chain H: R.43, Q.44 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain F: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain G: R.236 Chain J: R.250 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain G: K.256, H.257, V.258 Chain H: Q.44 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain H: H.231, P.232, Y.233 Chain I: M.66 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain H: K.138, S.139 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain H: T.137 Ligand excluded by PLIP CL.26: 7 residues within 4Å: Chain H: N.15, K.34 Chain I: G.27 Chain J: Q.76, N.82 Chain K: R.43, Q.44 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain I: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain J: R.236 Chain M: R.250 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain J: K.256, H.257, V.258 Chain K: Q.44 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain K: H.231, P.232, Y.233 Chain L: M.66 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain K: K.138, S.139 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain K: T.137 Ligand excluded by PLIP CL.35: 7 residues within 4Å: Chain K: N.15, K.34 Chain L: G.27 Chain M: Q.76, N.82 Chain N: R.43, Q.44 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain L: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain A: R.250 Chain M: R.236 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain M: K.256, H.257, V.258 Chain N: Q.44 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain N: H.231, P.232, Y.233 Chain O: M.66 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain N: K.138, S.139 Ligand excluded by PLIP CL.43: 1 residues within 4Å: Chain N: T.137 Ligand excluded by PLIP CL.44: 7 residues within 4Å: Chain A: Q.76, N.82 Chain B: R.43, Q.44 Chain N: N.15, K.34 Chain O: G.27 Ligand excluded by PLIP CL.45: 6 residues within 4Å: Chain O: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity. J.Virol. (2015)

Release Date

2015-08-26

Peptides

VP1: ADGJM
VP0: BEHKN
VP3: CFILO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

B
B

E
B

H
B

K
B

N
B

C
C

F
C

I
C

L
C

O
C

VP1

VP0

VP3

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