SMTL ID : 7c9w.3 (3 other biounits)

E30 F-particle in complex with CD55

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 13 residues within 4Å: Chain A: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.96, A:T.98, A:I.120, A:Y.147, A:Y.147, A:Y.147, A:I.184, A:I.184 Hydrogen bonds: A:R.99, A:R.99 SPH.3: 13 residues within 4Å: Chain F: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.96, F:T.98, F:I.120, F:Y.147, F:Y.147, F:Y.147, F:I.184, F:I.184 Hydrogen bonds: F:R.99, F:R.99 SPH.5: 13 residues within 4Å: Chain K: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:I.96, K:T.98, K:I.120, K:Y.147, K:Y.147, K:Y.147, K:I.184, K:I.184 Hydrogen bonds: K:R.99, K:R.99 SPH.7: 13 residues within 4Å: Chain P: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain P Hydrophobic interactions: P:I.96, P:T.98, P:I.120, P:Y.147, P:Y.147, P:Y.147, P:I.184, P:I.184 Hydrogen bonds: P:R.99, P:R.99 SPH.9: 13 residues within 4Å: Chain U: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain U Hydrophobic interactions: U:I.96, U:T.98, U:I.120, U:Y.147, U:Y.147, U:Y.147, U:I.184, U:I.184 Hydrogen bonds: U:R.99, U:R.99 SPH.11: 13 residues within 4Å: Chain Z: I.96, T.98, R.99, L.118, I.120, V.145, Y.147, P.169, M.182, I.184, Y.193, N.195, L.220 10 PLIP interactions: 10 interactions with chain Z Hydrophobic interactions: Z:I.96, Z:T.98, Z:I.120, Z:Y.147, Z:Y.147, Z:Y.147, Z:I.184, Z:I.184 Hydrogen bonds: Z:R.99, Z:R.99

6 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 9 residues within 4Å: Chain D: G.1, A.2, Y.31 Chain I: A.2, V.4, T.27, I.29, Y.31 Ligands: MYR.4 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: D:Y.31, I:A.2, I:T.27, I:I.29 MYR.4: 4 residues within 4Å: Chain I: G.1, A.2, Y.31 Ligands: MYR.2 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.31 MYR.6: 4 residues within 4Å: Chain N: G.1, A.2, Y.31 Ligands: MYR.8 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:Y.31 MYR.8: 9 residues within 4Å: Chain N: A.2, V.4, T.27, I.29, Y.31 Chain S: G.1, A.2, Y.31 Ligands: MYR.6 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain N Hydrophobic interactions: S:Y.31, N:A.2, N:T.27, N:I.29 MYR.10: 9 residues within 4Å: Chain 2: A.2, V.4, T.27, I.29, Y.31 Chain X: G.1, A.2, Y.31 Ligands: MYR.12 4 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain X Hydrophobic interactions: 2:A.2, 2:T.27, 2:I.29, X:Y.31 MYR.12: 4 residues within 4Å: Chain 2: G.1, A.2, Y.31 Ligands: MYR.10 1 PLIP interactions: 1 interactions with chain 2 Hydrophobic interactions: 2:Y.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K. et al., Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage. Nat Commun (2020)

Release Date

2020-07-29

Peptides

VP1: AFKPUZ
VP2: BGLQV0
VP3: CHMRW1
VP4: DINSX2
Complement decay-accelerating factor: EJOTY3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

Z
A

B
B

G
B

L
B

Q
B

V
B

0
B

C
C

H
C

M
C

R
C

W
C

1
C

D
D

I
D

N
D

S
D

X
D

2
D

E
E

J
E

O
E

T
E

Y
E

3
E

VP1

VP2

VP3

VP4

Complement decay-accelerating factor

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