SMTL ID : 6cvb.3 (3 other biounits)

CryoEM structure of human enterovirus D68 in complex with 6'-sialyl-N-acetyllactosamine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL-SIA.1: 13 residues within 4Å: Chain A: K.270, A.273, P.274, N.275, G.282 Chain B: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.91, B:D.91, B:R.95, B:R.104, B:P.231, B:D.232, A:K.270, A:N.275 Water bridges: B:R.104, B:R.104, A:K.270 Salt bridges: B:R.104 Hydrophobic interactions: A:P.274 NAG-GAL-SIA.2: 13 residues within 4Å: Chain E: K.270, A.273, P.274, N.275, G.282 Chain F: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:D.91, F:D.91, E:K.270, E:N.275, F:R.95, F:R.104, F:P.231, F:D.232 Hydrophobic interactions: E:P.274 Water bridges: E:K.270, F:R.104, F:R.104 Salt bridges: F:R.104 NAG-GAL-SIA.3: 13 residues within 4Å: Chain I: K.270, A.273, P.274, N.275, G.282 Chain J: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:D.91, J:D.91, J:R.95, J:R.104, J:P.231, J:D.232, I:K.270, I:N.275 Water bridges: J:R.104, J:R.104, I:K.270 Salt bridges: J:R.104 Hydrophobic interactions: I:P.274 NAG-GAL-SIA.4: 13 residues within 4Å: Chain M: K.270, A.273, P.274, N.275, G.282 Chain N: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain N, 4 interactions with chain M Hydrogen bonds: N:D.91, N:D.91, M:K.270, M:N.275, N:R.95, N:R.104, N:P.231, N:D.232 Hydrophobic interactions: M:P.274 Water bridges: M:K.270, N:R.104, N:R.104 Salt bridges: N:R.104 NAG-GAL-SIA.5: 13 residues within 4Å: Chain Q: K.270, A.273, P.274, N.275, G.282 Chain R: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain R, 4 interactions with chain Q Hydrogen bonds: R:D.91, R:D.91, Q:K.270, Q:N.275, R:R.95, R:R.104, R:P.231, R:D.232 Hydrophobic interactions: Q:P.274 Water bridges: Q:K.270, R:R.104, R:R.104 Salt bridges: R:R.104 NAG-GAL-SIA.6: 13 residues within 4Å: Chain U: K.270, A.273, P.274, N.275, G.282 Chain V: D.91, R.95, R.104, N.180, P.231, D.232, I.233, G.234 11 PLIP interactions: 7 interactions with chain V, 4 interactions with chain U Hydrogen bonds: V:D.91, V:D.91, U:K.270, U:N.275, V:R.95, V:R.104, V:P.231, V:D.232 Hydrophobic interactions: U:P.274 Water bridges: U:K.270, V:R.104, V:R.104 Salt bridges: V:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baggen, J. et al., Bypassing pan-enterovirus host factor PLA2G16. Nat Commun (2019)

Release Date

2019-07-24

Peptides

viral protein 1: AEIMQU
viral protein 3: BFJNRV
viral protein 2: CGKOSW
viral protein 4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

viral protein 1

viral protein 3

viral protein 2

viral protein 4

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