SMTL ID : 8ufc.1

Eastern equine encephalitis virus (PE-6) VLP in complex with VLDLR LA(1-2) (asymmetric unit)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-mer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.134, W.142, S.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 NAG.2: 2 residues within 4Å: Chain B: T.313, N.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.313, B:N.315 NAG.3: 3 residues within 4Å: Chain D: N.134, W.142, S.144 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.134 NAG.4: 4 residues within 4Å: Chain E: K.276, I.281, T.313, N.315 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain G: M.132, N.134, W.142, S.144 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.134 NAG.6: 3 residues within 4Å: Chain H: I.281, T.313, N.315 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain J: N.134, W.142, S.144 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.134 NAG.8: 3 residues within 4Å: Chain K: I.281, T.313, N.315 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.281

8 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain M: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.20, M:D.23, M:D.25, M:D.27, M:D.33 CA.10: 6 residues within 4Å: Chain M: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.59, M:D.62, M:D.64, M:D.66, M:E.73 CA.11: 7 residues within 4Å: Chain K: K.156 Chain N: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.20, N:D.23, N:D.25, N:D.33, N:E.34 CA.12: 6 residues within 4Å: Chain N: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.59, N:D.62, N:D.64, N:D.66, N:E.73 CA.13: 7 residues within 4Å: Chain E: K.156 Chain O: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.20, O:D.25, O:D.27, O:D.33, O:E.34 CA.14: 6 residues within 4Å: Chain O: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.59, O:D.64, O:D.66, O:D.72, O:E.73 CA.15: 8 residues within 4Å: Chain B: K.156 Chain P: W.20, C.22, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.20, P:D.23, P:D.25, P:D.27, P:D.33 CA.16: 7 residues within 4Å: Chain B: K.231 Chain P: W.59, D.62, D.64, D.66, D.72, E.73 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.59, P:D.64, P:D.66, P:D.72, P:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, L.J. et al., Structural and functional basis of VLDLR usage by Eastern equine encephalitis virus. Cell (2024)

Release Date

2024-01-17

Peptides

E1 protein: ADGJ
E2 protein: BEHK
Capsid protein: CFIL
Very low-density lipoprotein receptor: MNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

M
V

N
W

O
X

P
Y

Membrane

We predict this structure to be a membrane protein.
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E1 protein

E2 protein

Capsid protein

Very low-density lipoprotein receptor

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