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

Crystal structure of empty coxsackievirus A16 particle

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-6-6-6-mer

Ligands

6 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 SPH.46: 10 residues within 4Å: Chain P: 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 P Hydrophobic interactions: P:L.113, P:F.135, P:Y.155, P:Y.155, P:W.203, P:N.228, P:F.233 Hydrogen bonds: P:D.112, P:L.113 Water bridges: P:Q.224, P:N.228

6 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain F: K.7, P.8 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:P.8 K.11: 3 residues within 4Å: Chain D: Q.189 Chain F: V.20, S.21 No protein-ligand interaction detected (PLIP) K.20: 3 residues within 4Å: Chain G: Q.189 Chain I: V.20, S.21 No protein-ligand interaction detected (PLIP) K.29: 5 residues within 4Å: Chain I: K.7, P.8 Chain J: Q.189 Chain L: V.20, S.21 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:P.8 K.38: 5 residues within 4Å: Chain M: Q.189 Chain O: V.20, S.21 Chain R: K.7, P.8 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:P.8 K.47: 3 residues within 4Å: Chain P: Q.189 Chain R: V.20, S.21 No protein-ligand interaction detected (PLIP)

42 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: 2 residues within 4Å: Chain B: T.137 Chain O: T.79 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: 1 residues within 4Å: Chain D: R.236 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: 3 residues within 4Å: Chain E: N.15, K.34 Chain F: G.27 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: 1 residues within 4Å: Chain G: R.236 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: 3 residues within 4Å: Chain H: N.15, K.34 Chain I: G.27 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 G: R.250 Chain J: R.236 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: 2 residues within 4Å: Chain C: T.79 Chain K: T.137 Ligand excluded by PLIP CL.35: 7 residues within 4Å: Chain G: Q.76, N.82 Chain H: R.43, Q.44 Chain K: N.15, K.34 Chain L: G.27 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 M: R.236 Chain P: R.250 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: 2 residues within 4Å: Chain L: T.79 Chain N: T.137 Ligand excluded by PLIP CL.44: 7 residues within 4Å: Chain N: N.15, K.34 Chain O: G.27 Chain P: Q.76, N.82 Chain Q: R.43, Q.44 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 CL.48: 1 residues within 4Å: Chain P: R.236 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain P: K.256, H.257, V.258 Chain Q: Q.44 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain Q: H.231, P.232, Y.233 Chain R: M.66 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain Q: K.138, S.139 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain Q: T.137 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain Q: N.15, K.34 Chain R: G.27 Ligand excluded by PLIP CL.54: 6 residues within 4Å: Chain R: 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: ADGJMP
VP0: BEHKNQ
VP3: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

P
A

B
B

E
B

H
B

K
B

N
B

Q
B

C
C

F
C

I
C

L
C

O
C

R
C

VP1

VP0

VP3

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