SMTL ID : 8ufb.1

Eastern equine encephalitis virus (PE-6) VLP in complex with full-length VLDLR (asymmetric unit)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-8-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: 3 residues within 4Å: Chain B: I.281, 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: 2 residues within 4Å: Chain K: I.281, N.315 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.281

12 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain M: W.23, D.26, D.28, D.30, D.36, E.37 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.23, M:D.26, M:D.28, M:D.30, M:D.36 CA.10: 6 residues within 4Å: Chain M: W.62, D.65, D.67, D.69, D.75, E.76 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:W.62, M:D.65, M:D.67, M:D.69, M:E.76 CA.11: 7 residues within 4Å: Chain K: K.156 Chain N: W.23, D.26, D.28, D.30, D.36, E.37 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.23, N:D.26, N:D.28, N:D.36, N:E.37 CA.12: 6 residues within 4Å: Chain N: W.62, D.65, D.67, D.69, D.75, E.76 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:W.62, N:D.65, N:D.67, N:D.69, N:E.76 CA.13: 7 residues within 4Å: Chain E: K.156 Chain O: W.23, D.26, D.28, D.30, D.36, E.37 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.23, O:D.26, O:D.28, O:D.30, O:D.36 CA.14: 6 residues within 4Å: Chain O: W.62, D.65, D.67, D.69, D.75, E.76 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.62, O:D.65, O:D.67, O:D.69, O:E.76 CA.15: 8 residues within 4Å: Chain B: K.156 Chain P: W.23, C.25, D.26, D.28, D.30, D.36, E.37 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.23, P:D.26, P:D.28, P:D.30, P:D.36 CA.16: 7 residues within 4Å: Chain B: K.231 Chain P: W.62, D.65, D.67, D.69, D.75, E.76 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.62, P:D.67, P:D.69, P:D.75, P:E.76 CA.17: 7 residues within 4Å: Chain H: K.206 Chain Q: W.229, D.232, D.234, D.236, D.242, E.243 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:W.229, Q:D.234, Q:D.236, Q:D.242, Q:E.243 CA.18: 7 residues within 4Å: Chain K: K.206 Chain R: W.229, D.232, D.234, D.236, D.242, E.243 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:W.229, R:D.232, R:D.234, R:D.242, R:E.243 CA.19: 7 residues within 4Å: Chain E: K.206 Chain S: W.229, D.232, D.234, D.236, D.242, E.243 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:W.229, S:D.234, S:D.236, S:D.242, S:E.243 CA.20: 7 residues within 4Å: Chain B: K.206 Chain T: W.229, D.232, D.234, D.236, D.242, E.243 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:W.229, T:D.234, T:D.236, T:D.242, T:E.243

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
Isoform Short of Very low-density lipoprotein receptor: MNOPQRST

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

Q
R

R
S

S
T

T
U

Membrane

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

E2 protein

Capsid protein

Isoform Short of Very low-density lipoprotein receptor

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