SMTL ID : 8gsd.3 (3 other biounits)

Echovirus3 full particle in complex with 6D10 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-6-6-mer

Ligands

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 14 residues within 4Å: Chain C: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.95, C:T.97, C:I.119, C:I.144, C:Y.146, C:V.183, C:V.183, C:I.186, C:F.240 Hydrogen bonds: C:S.193, C:N.194 SPH.2: 14 residues within 4Å: Chain I: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:I.95, I:T.97, I:I.119, I:I.144, I:Y.146, I:V.183, I:V.183, I:I.186, I:F.240 Hydrogen bonds: I:S.193, I:N.194 SPH.3: 14 residues within 4Å: Chain O: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain O Hydrophobic interactions: O:I.95, O:T.97, O:I.119, O:I.144, O:Y.146, O:V.183, O:V.183, O:I.186, O:F.240 Hydrogen bonds: O:S.193, O:N.194 SPH.4: 14 residues within 4Å: Chain U: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain U Hydrophobic interactions: U:I.95, U:T.97, U:I.119, U:I.144, U:Y.146, U:V.183, U:V.183, U:I.186, U:F.240 Hydrogen bonds: U:S.193, U:N.194 SPH.5: 14 residues within 4Å: Chain 0: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain 0 Hydrophobic interactions: 0:I.95, 0:T.97, 0:I.119, 0:I.144, 0:Y.146, 0:V.183, 0:V.183, 0:I.186, 0:F.240 Hydrogen bonds: 0:S.193, 0:N.194 SPH.6: 14 residues within 4Å: Chain 6: I.95, T.97, R.98, I.119, I.144, Y.146, M.181, V.183, I.186, Y.192, S.193, N.194, M.216, F.240 11 PLIP interactions: 11 interactions with chain 6 Hydrophobic interactions: 6:I.95, 6:T.97, 6:I.119, 6:I.144, 6:Y.146, 6:V.183, 6:V.183, 6:I.186, 6:F.240 Hydrogen bonds: 6:S.193, 6:N.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qi, S. et al., Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody. Viruses (2022)

Release Date

2022-12-14

Peptides

Heavy chain of 6D10: AGMSY4
Light chain of 6D10: BHNTZ5
Genome polyprotein (Fragment): CIOU06
Genome polyprotein: DJPV17
Genome polyprotein: EKQW28
Genome polyprotein (Fragment): FLRX39

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

G
H

M
H

S
H

Y
H

4
H

B
L

H
L

N
L

T
L

Z
L

5
L

C
1

I
1

O
1

U
1

0
1

6
1

D
2

J
2

P
2

V
2

1
2

7
2

E
3

K
3

Q
3

W
3

2
3

8
3

F
4

L
4

R
4

X
4

3
4

9
4

Heavy chain of 6D10

Light chain of 6D10

Genome polyprotein (Fragment)

Genome polyprotein

Genome polyprotein

Genome polyprotein (Fragment)

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