SMTL ID : 5c8c.3 (3 other biounits)

Crystal structure of recombinant coxsackievirus A16 capsid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-6-6-6-mer

Ligands

6 x STE: STEARIC ACID(Non-covalent)

STE.1: 17 residues within 4Å: Chain A: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.111, A:L.113, A:F.135, A:F.137, A:Y.155, A:V.179, A:V.190, A:V.192, A:Y.201, A:Y.201, A:W.203, A:N.228, A:F.233, A:F.233 Hydrogen bonds: A:L.113 STE.5: 17 residues within 4Å: Chain D: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.111, D:L.113, D:F.135, D:F.137, D:Y.155, D:V.179, D:V.190, D:V.192, D:Y.201, D:Y.201, D:W.203, D:N.228, D:F.233, D:F.233 Hydrogen bonds: D:L.113 STE.9: 17 residues within 4Å: Chain G: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:I.111, G:L.113, G:F.135, G:F.137, G:Y.155, G:V.179, G:V.190, G:V.192, G:Y.201, G:Y.201, G:W.203, G:N.228, G:F.233, G:F.233 Hydrogen bonds: G:D.112, G:L.113 STE.13: 17 residues within 4Å: Chain J: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:I.111, J:L.113, J:F.135, J:F.137, J:Y.155, J:V.179, J:V.190, J:V.192, J:Y.201, J:Y.201, J:W.203, J:N.228, J:F.233, J:F.233 Hydrogen bonds: J:L.113 STE.17: 17 residues within 4Å: Chain M: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 16 PLIP interactions: 16 interactions with chain M Hydrophobic interactions: M:I.111, M:L.113, M:F.135, M:F.137, M:Y.155, M:V.179, M:V.190, M:V.192, M:Y.201, M:Y.201, M:W.203, M:N.228, M:F.233, M:F.233 Hydrogen bonds: M:D.112, M:L.113 STE.21: 17 residues within 4Å: Chain P: I.111, D.112, L.113, F.135, F.137, Y.153, Y.155, P.177, V.179, V.190, V.192, M.195, Y.201, W.203, N.228, M.230, F.233 16 PLIP interactions: 16 interactions with chain P Hydrophobic interactions: P:I.111, P:L.113, P:F.135, P:F.137, P:Y.155, P:V.179, P:V.190, P:V.192, P:Y.201, P:Y.201, P:W.203, P:N.228, P:F.233, P:F.233 Hydrogen bonds: P:D.112, P:L.113

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

CL.2: 1 residues within 4Å: Chain A: R.250 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: T.203, I.204 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.236 Chain D: R.250 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain E: T.203, I.204 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain G: R.250 Chain J: R.236 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain H: T.203, I.204 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain J: R.250 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain K: T.203, I.204 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain M: R.250 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain N: T.203, I.204 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain M: R.236 Chain P: R.250 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain Q: T.203, I.204 Ligand excluded by PLIP

6 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (PLIP) K.7: 4 residues within 4Å: Chain D: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain G: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain J: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (PLIP) K.19: 4 residues within 4Å: Chain M: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (PLIP) K.23: 4 residues within 4Å: Chain P: T.28, A.29, N.31, N.71 No protein-ligand interaction detected (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

2015-09-30

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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