SMTL ID : 9dqz.1

Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-4-4-4-4-mer

Ligands

16 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.1: 2 residues within 4Å: Chain A: N.139, H.327 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.245 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain B: G.194, N.196 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain B: N.318 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain D: N.139, H.327 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain D: N.245 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain E: N.196 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain E: W.279, T.284, N.318 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain G: N.139, H.327 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain G: N.245 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain H: G.194, N.196 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain H: W.279, T.284, N.318 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain M: N.139, H.327 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain M: N.245 Chain N: R.131 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain N: G.194, N.196, S.212 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain N: N.318 Ligand excluded by PLIP

8 x CA: CALCIUM ION

CA.13: 6 residues within 4Å: Chain J: W.18, D.21, D.23, D.25, D.31, E.32 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:W.18, J:D.21, J:D.23, J:D.31, J:E.32 CA.14: 7 residues within 4Å: Chain B: K.190 Chain J: W.57, D.60, D.62, D.64, D.70, E.71 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:W.57, J:D.60, J:D.60, J:D.64, J:D.70 CA.15: 6 residues within 4Å: Chain K: W.18, D.21, D.23, D.25, D.31, E.32 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:W.18, K:D.21, K:D.23, K:D.31 CA.16: 4 residues within 4Å: Chain K: W.57, D.60, D.62, D.64 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.60, K:D.60, K:D.64 CA.17: 6 residues within 4Å: Chain L: W.18, D.21, D.23, D.25, D.31, E.32 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:W.18, L:D.21, L:D.23, L:D.25, L:D.31 CA.18: 5 residues within 4Å: Chain L: W.57, D.60, D.62, D.64, D.70 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:W.57, L:D.60, L:D.64, L:D.64, L:D.70 CA.23: 6 residues within 4Å: Chain P: W.18, D.21, D.23, D.25, D.31, E.32 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:W.18, P:D.21, P:D.23, P:D.25, P:D.31 CA.24: 3 residues within 4Å: Chain N: K.190 Chain P: D.60, D.62 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abraham, J. et al., Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR. To Be Published

Release Date

2025-03-26

Peptides

Structural polyprotein: ADGM
Structural polyprotein: BEHN
Capsid protein: CFIO
Very low-density lipoprotein receptor: JKLP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
G

G
J

M
A

B
E

E
H

H
K

N
B

C
F

F
I

I
L

O
C

J
M

K
N

L
O

P
P

Membrane

We predict this structure to be a membrane protein.
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Structural polyprotein

Structural polyprotein

Capsid protein

Very low-density lipoprotein receptor