SMTL ID : 7eak.2 (3 other biounits)

Echovirus3 full particle in complex with 5G3 fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Covalent)

SPH.1: 15 residues within 4Å: Chain A: I.95, T.97, M.117, I.119, I.144, M.145, Y.146, P.168, S.169, I.170, M.181, V.183, I.186, Y.192, M.216 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.95, A:I.144, A:Y.146, A:Y.146, A:I.170, A:V.183, A:V.183, A:I.186 SPH.3: 15 residues within 4Å: Chain G: I.95, T.97, M.117, I.119, I.144, M.145, Y.146, P.168, S.169, I.170, M.181, V.183, I.186, Y.192, M.216 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.95, G:I.144, G:Y.146, G:Y.146, G:I.170, G:V.183, G:V.183, G:I.186 SPH.5: 15 residues within 4Å: Chain M: I.95, T.97, M.117, I.119, I.144, M.145, Y.146, P.168, S.169, I.170, M.181, V.183, I.186, Y.192, M.216 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:I.95, M:I.144, M:Y.146, M:Y.146, M:I.170, M:V.183, M:V.183, M:I.186 SPH.7: 15 residues within 4Å: Chain S: I.95, T.97, M.117, I.119, I.144, M.145, Y.146, P.168, S.169, I.170, M.181, V.183, I.186, Y.192, M.216 8 PLIP interactions: 8 interactions with chain S Hydrophobic interactions: S:I.95, S:I.144, S:Y.146, S:Y.146, S:I.170, S:V.183, S:V.183, S:I.186 SPH.9: 15 residues within 4Å: Chain Y: I.95, T.97, M.117, I.119, I.144, M.145, Y.146, P.168, S.169, I.170, M.181, V.183, I.186, Y.192, M.216 8 PLIP interactions: 8 interactions with chain Y Hydrophobic interactions: Y:I.95, Y:I.144, Y:Y.146, Y:Y.146, Y:I.170, Y:V.183, Y:V.183, Y:I.186

5 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 10 residues within 4Å: Chain D: G.1, A.2, Y.31 Chain J: A.2, T.27, I.29, Y.31 Chain U: L.2 Ligands: MYR.4, MYR.10 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain U, 3 interactions with chain J Hydrophobic interactions: D:Y.31, U:L.2, J:A.2, J:I.29, J:Y.31 MYR.4: 10 residues within 4Å: Chain 0: L.2 Chain J: G.1, A.2, Y.31 Chain P: A.2, T.27, I.29, Y.31 Ligands: MYR.2, MYR.6 5 PLIP interactions: 3 interactions with chain P, 1 interactions with chain J, 1 interactions with chain 0 Hydrophobic interactions: P:A.2, P:I.29, P:Y.31, J:Y.31, 0:L.2 MYR.6: 10 residues within 4Å: Chain C: L.2 Chain P: G.1, A.2, Y.31 Chain V: A.2, T.27, I.29, Y.31 Ligands: MYR.4, MYR.8 5 PLIP interactions: 1 interactions with chain P, 1 interactions with chain C, 3 interactions with chain V Hydrophobic interactions: P:Y.31, C:L.2, V:A.2, V:I.29, V:Y.31 MYR.8: 10 residues within 4Å: Chain 1: A.2, T.27, I.29, Y.31 Chain I: L.2 Chain V: G.1, A.2, Y.31 Ligands: MYR.6, MYR.10 5 PLIP interactions: 1 interactions with chain V, 1 interactions with chain I, 3 interactions with chain 1 Hydrophobic interactions: V:Y.31, I:L.2, 1:A.2, 1:I.29, 1:Y.31 MYR.10: 10 residues within 4Å: Chain 1: G.1, A.2, Y.31 Chain D: A.2, T.27, I.29, Y.31 Chain O: L.2 Ligands: MYR.2, MYR.8 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain O, 1 interactions with chain 1 Hydrophobic interactions: D:A.2, D:I.29, D:Y.31, O:L.2, 1:Y.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, R. et al., Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody. Cell Discov (2021)

Release Date

2021-07-14

Peptides

Capsid protein VP1: AGMSY
Capsid protein VP2: BHNTZ
Capsid protein VP3: CIOU0
Capsid protein VP4: DJPV1
heavy chain of 5G3 fab: EKQW2
light chain of 5G3 fab: FLRX3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

S
A

Y
A

B
B

H
B

N
B

T
B

Z
B

C
C

I
C

O
C

U
C

0
C

D
D

J
D

P
D

V
D

1
D

E
F

K
F

Q
F

W
F

2
F

F
L

L
L

R
L

X
L

3
L

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

heavy chain of 5G3 fab

light chain of 5G3 fab

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