SMTL ID : 8yw1.1

Semliki Forest virus viron in complex with VLDLR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-1-8-8-mer

Ligands

24 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: H.116, N.264 Chain B: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: C.63, F.95 Chain B: N.196, T.198 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain E: R.134, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 1 residues within 4Å: Chain F: N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain G: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain E: H.116, E.209, N.264 Chain H: L.256, D.257, N.258 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.209 NAG-NAG-BMA.8: 3 residues within 4Å: Chain E: F.95 Chain H: N.196, V.204 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain F: R.115, H.116 Chain I: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain F: C.63, F.95 Chain I: N.196, T.198, V.204, Q.220 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain G: H.116, N.264 Chain J: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain G: C.63, F.95 Chain J: N.196, V.204 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain R: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain R: H.116, N.264 Chain S: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain R: C.63, F.95 Chain S: N.196, T.198 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain U: R.134, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 1 residues within 4Å: Chain V: N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 3 residues within 4Å: Chain W: R.134, M.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 6 residues within 4Å: Chain U: H.116, E.209, N.264 Chain X: L.256, D.257, N.258 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:E.209 NAG-NAG-BMA.20: 3 residues within 4Å: Chain U: F.95 Chain X: N.196, V.204 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain V: R.115, H.116 Chain Y: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 6 residues within 4Å: Chain V: C.63, F.95 Chain Y: N.196, T.198, V.204, Q.220 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain W: H.116, N.264 Chain Z: L.256, D.257, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 4 residues within 4Å: Chain W: C.63, F.95 Chain Z: N.196, V.204 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, T., Structure of Semliki Forest virus at 3.02 Angstroms resolution. To Be Published

Release Date

2024-12-11

Peptides

Spike glycoprotein E1: AEFGRUVW
Spike glycoprotein E2: BHIJSXYZ
Very low-density lipoprotein receptor: C
capsid protein, partial: DNOPT345
Spike glycoprotein E3: KLMQ0126

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
F

F
G

G
H

R
E

U
U

V
V

W
W

B
B

H
I

I
J

J
K

S
R

X
X

Y
Y

Z
Z

C
C

D
D

N
O

O
P

P
Q

T
T

3
d

4
e

5
f

K
L

L
M

M
N

Q
S

0
a

1
b

2
c

6
g

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Spike glycoprotein E1

Spike glycoprotein E2

Very low-density lipoprotein receptor

capsid protein, partial

Spike glycoprotein E3

Related Entries With Identical Sequence