SMTL ID : 5bno.3 (4 other biounits)

Crystal structure of human enterovirus D68 in complex with 6'SLN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

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: 11 residues within 4Å: Chain A: P.274, N.275, G.282 Chain C: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Water bridges: A:N.283, C:R.95 Hydrogen bonds: C:D.91, C:D.91, C:P.231, C:D.232, C:D.232, A:N.275 Salt bridges: C:R.104 NAG-GAL-SIA.2: 11 residues within 4Å: Chain E: P.274, N.275, G.282 Chain G: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain G Water bridges: E:N.283, G:R.95 Hydrogen bonds: G:D.91, G:D.91, G:P.231, G:D.232, G:D.232, E:N.275 Salt bridges: G:R.104 NAG-GAL-SIA.3: 11 residues within 4Å: Chain I: P.274, N.275, G.282 Chain K: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:D.91, K:D.91, K:P.231, K:D.232, K:D.232, I:N.275 Water bridges: I:N.283, K:R.95 Salt bridges: K:R.104 NAG-GAL-SIA.4: 11 residues within 4Å: Chain M: P.274, N.275, G.282 Chain O: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 5 interactions with chain O, 1 interactions with chain M Hydrogen bonds: O:D.91, O:D.91, O:P.231, O:D.232, O:D.232, M:N.275 Water bridges: M:N.283, O:R.95 Salt bridges: O:R.104 NAG-GAL-SIA.5: 11 residues within 4Å: Chain Q: P.274, N.275, G.282 Chain S: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 1 interactions with chain Q, 5 interactions with chain S Water bridges: Q:N.283, S:R.95 Hydrogen bonds: S:D.91, S:D.91, S:P.231, S:D.232, S:D.232, Q:N.275 Salt bridges: S:R.104 NAG-GAL-SIA.6: 11 residues within 4Å: Chain U: P.274, N.275, G.282 Chain W: D.91, R.95, R.104, S.180, P.231, D.232, I.233, G.234 6 PLIP interactions: 1 interactions with chain U, 5 interactions with chain W Water bridges: U:N.283, W:R.95 Hydrogen bonds: W:D.91, W:D.91, W:P.231, W:D.232, W:D.232, U:N.275 Salt bridges: W:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Sialic acid-dependent cell entry of human enterovirus D68. Nat Commun (2015)

Release Date

2015-11-18

Peptides

Capsid protein VP1: AEIMQU
Capsid protein VP2: BFJNRV
Capsid protein VP3: CGKOSW
Capsid protein VP4: 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

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

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