SMTL ID : 6odf.2 (3 other biounits)

EEEV glycoproteins bound with heparan sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-20-20-mer

Ligands

30 x U9A- U97: 2-O-sulfo-beta-L-galactopyranuronic acid-(1-4)-[(2R,3R,4R,5R,6R)-2,4,5-trihydroxy-6-(sulfooxy)tetrahydro-2H-pyran-3-yl]sulfamic acid(Non-covalent)

U9A-U97.1: 3 residues within 4Å: Chain B: N.80, H.82, H.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.80, B:H.114, B:N.80 Salt bridges: B:H.114, B:H.82 U9A-U97.2: 10 residues within 4Å: Chain B: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.93, B:S.93, B:H.94, B:R.157, B:L.2, B:D.3, B:R.157, B:A.158 Salt bridges: B:R.157 U9A-U97.3: 8 residues within 4Å: Chain D: N.80, H.82, H.114 Chain F: H.82, H.114 Chain H: H.82, H.114, R.119 8 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 4 interactions with chain H Hydrogen bonds: D:N.80, D:H.114, D:N.80 Salt bridges: D:H.114, F:H.82, D:H.82, F:H.82, F:H.114, H:H.82, H:H.82, H:H.114, H:H.114 U9A-U97.4: 10 residues within 4Å: Chain D: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.93, D:S.93, D:H.94, D:R.157, D:D.3, D:T.4, D:R.157, D:A.158 Salt bridges: D:R.157 U9A-U97.5: 10 residues within 4Å: Chain F: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.93, F:S.93, F:H.94, F:R.157, F:L.2, F:D.3, F:R.157, F:A.158 Salt bridges: F:R.157 U9A-U97.6: 10 residues within 4Å: Chain H: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.93, H:S.93, H:H.94, H:R.157, H:L.2, H:D.3, H:T.4, H:R.157, H:A.158 Salt bridges: H:R.157 U9A-U97.7: 3 residues within 4Å: Chain J: N.80, H.82, H.114 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.80, J:H.114, J:N.80 Salt bridges: J:H.114, J:H.82 U9A-U97.8: 10 residues within 4Å: Chain J: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:S.93, J:S.93, J:H.94, J:R.157, J:D.3, J:T.4, J:R.157, J:A.158 Salt bridges: J:R.157 U9A-U97.9: 8 residues within 4Å: Chain L: N.80, H.82, H.114 Chain N: H.82, H.114 Chain P: H.82, H.114, R.119 8 PLIP interactions: 2 interactions with chain L, 2 interactions with chain N, 4 interactions with chain P Hydrogen bonds: L:N.80, L:H.114, L:N.80 Salt bridges: L:H.114, N:H.82, L:H.82, P:H.82, P:H.82, P:H.114, P:H.114, N:H.82, N:H.114 U9A-U97.10: 10 residues within 4Å: Chain L: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:S.93, L:S.93, L:H.94, L:R.157, L:L.2, L:D.3, L:R.157, L:A.158 Salt bridges: L:R.157 U9A-U97.11: 10 residues within 4Å: Chain N: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:S.93, N:S.93, N:H.94, N:R.157, N:L.2, N:D.3, N:T.4, N:R.157, N:A.158 Salt bridges: N:R.157 U9A-U97.12: 10 residues within 4Å: Chain P: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain P Hydrogen bonds: P:S.93, P:S.93, P:H.94, P:R.157, P:D.3, P:T.4, P:R.157, P:A.158 Salt bridges: P:R.157 U9A-U97.13: 3 residues within 4Å: Chain R: N.80, H.82, H.114 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:N.80, R:H.114, R:N.80 Salt bridges: R:H.114, R:H.82 U9A-U97.14: 10 residues within 4Å: Chain R: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain R Hydrogen bonds: R:S.93, R:S.93, R:H.94, R:R.157, R:D.3, R:T.4, R:R.157, R:A.158 Salt bridges: R:R.157 U9A-U97.15: 8 residues within 4Å: Chain T: N.80, H.82, H.114 Chain V: H.82, H.114 Chain X: H.82, H.114, R.119 8 PLIP interactions: 2 interactions with chain V, 2 interactions with chain T, 4 interactions with chain X Salt bridges: V:H.82, T:H.114, T:H.82, V:H.82, V:H.114, X:H.82, X:H.82, X:H.114, X:H.114 Hydrogen bonds: T:N.80, T:H.114, T:N.80 U9A-U97.16: 10 residues within 4Å: Chain T: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain T Hydrogen bonds: T:S.93, T:S.93, T:H.94, T:R.157, T:L.2, T:D.3, T:R.157, T:A.158 Salt bridges: T:R.157 U9A-U97.17: 10 residues within 4Å: Chain V: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain V Hydrogen bonds: V:S.93, V:S.93, V:H.94, V:R.157, V:D.3, V:T.4, V:R.157, V:A.158 Salt bridges: V:R.157 U9A-U97.18: 10 residues within 4Å: Chain X: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 4 PLIP interactions: 4 interactions with chain X Hydrogen bonds: X:S.93, X:S.93, X:H.94, X:R.157, X:D.3, X:R.157, X:A.158 Salt bridges: X:R.157 U9A-U97.19: 3 residues within 4Å: Chain Z: N.80, H.82, H.114 2 PLIP interactions: 2 interactions with chain Z Hydrogen bonds: Z:N.80, Z:H.114, Z:N.80 Salt bridges: Z:H.114, Z:H.82 U9A-U97.20: 10 residues within 4Å: Chain Z: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 4 PLIP interactions: 4 interactions with chain Z Hydrogen bonds: Z:S.93, Z:S.93, Z:H.94, Z:R.157, Z:D.3, Z:R.157, Z:A.158 Salt bridges: Z:R.157 U9A-U97.21: 8 residues within 4Å: Chain 1: N.80, H.82, H.114 Chain 3: H.82, H.114 Chain 5: H.82, H.114, R.119 8 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain 1, 4 interactions with chain 5 Salt bridges: 3:H.82, 1:H.114, 1:H.82, 3:H.82, 3:H.114, 5:H.82, 5:H.82, 5:H.114, 5:H.114 Hydrogen bonds: 1:N.80, 1:H.114, 1:N.80 U9A-U97.22: 10 residues within 4Å: Chain 1: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 6 PLIP interactions: 6 interactions with chain 1 Hydrogen bonds: 1:S.93, 1:S.93, 1:H.94, 1:R.157, 1:L.2, 1:D.3, 1:T.4, 1:R.157, 1:A.158 Salt bridges: 1:R.157 U9A-U97.23: 10 residues within 4Å: Chain 3: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain 3 Hydrogen bonds: 3:S.93, 3:S.93, 3:H.94, 3:R.157, 3:D.3, 3:T.4, 3:R.157, 3:A.158 Salt bridges: 3:R.157 U9A-U97.24: 10 residues within 4Å: Chain 5: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain 5 Hydrogen bonds: 5:S.93, 5:S.93, 5:H.94, 5:R.157, 5:L.2, 5:D.3, 5:R.157, 5:A.158 Salt bridges: 5:R.157 U9A-U97.25: 3 residues within 4Å: Chain 7: N.80, H.82, H.114 2 PLIP interactions: 2 interactions with chain 7 Hydrogen bonds: 7:N.80, 7:H.114, 7:N.80 Salt bridges: 7:H.114, 7:H.82 U9A-U97.26: 10 residues within 4Å: Chain 7: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 4 PLIP interactions: 4 interactions with chain 7 Hydrogen bonds: 7:S.93, 7:S.93, 7:H.94, 7:R.157, 7:D.3, 7:R.157, 7:A.158 Salt bridges: 7:R.157 U9A-U97.27: 8 residues within 4Å: Chain 9: N.80, H.82, H.114 Chain b: H.82, H.114 Chain d: H.82, H.114, R.119 8 PLIP interactions: 2 interactions with chain 9, 2 interactions with chain b, 4 interactions with chain d Hydrogen bonds: 9:N.80, 9:H.114, 9:N.80 Salt bridges: 9:H.114, b:H.82, 9:H.82, d:H.82, d:H.82, d:H.114, d:H.114, b:H.82, b:H.114 U9A-U97.28: 10 residues within 4Å: Chain 9: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 6 PLIP interactions: 6 interactions with chain 9 Hydrogen bonds: 9:S.93, 9:S.93, 9:H.94, 9:R.157, 9:L.2, 9:D.3, 9:T.4, 9:R.157, 9:A.158 Salt bridges: 9:R.157 U9A-U97.29: 10 residues within 4Å: Chain b: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 4 PLIP interactions: 4 interactions with chain b Hydrogen bonds: b:S.93, b:S.93, b:H.94, b:R.157, b:D.3, b:R.157, b:A.158 Salt bridges: b:R.157 U9A-U97.30: 10 residues within 4Å: Chain d: L.2, D.3, T.4, L.62, S.93, H.94, H.155, K.156, R.157, A.158 5 PLIP interactions: 5 interactions with chain d Hydrogen bonds: d:S.93, d:S.93, d:H.94, d:R.157, d:L.2, d:D.3, d:R.157, d:A.158 Salt bridges: d:R.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C.L. et al., Cryo-EM structure of eastern equine encephalitis virus in complex with heparan sulfate analogues. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-04-01

Peptides

E1: ACEGIKMOQSUWY02468ac
E2: BDFHJLNPRTVXZ13579bd

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
A

K
C

M
E

O
G

Q
A

S
C

U
E

W
G

Y
A

0
C

2
E

4
G

6
A

8
C

a
E

c
G

B
B

D
D

F
F

H
H

J
B

L
D

N
F

P
H

R
B

T
D

V
F

X
H

Z
B

1
D

3
F

5
H

7
B

9
D

b
F

d
H

E1

E2

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