SMTL ID : 7n1h.1 (1 other biounit)

CryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: W.20, D.23, L.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:W.20, A:D.23, A:L.25, A:D.27, A:D.33, A:E.34 CA.2: 6 residues within 4Å: Chain B: W.20, D.23, L.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.20, B:D.23, B:L.25, B:D.27, B:D.33, B:E.34 CA.3: 6 residues within 4Å: Chain C: W.20, D.23, L.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:W.20, C:D.23, C:L.25, C:D.27, C:D.33, C:E.34 CA.4: 6 residues within 4Å: Chain D: W.20, D.23, L.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:W.20, D:D.23, D:L.25, D:D.27, D:D.33, D:E.34

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

NAG.5: 3 residues within 4Å: Chain E: N.134, T.136, S.141 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.136 NAG.6: 2 residues within 4Å: Chain F: S.284, N.318 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.284 NAG.7: 3 residues within 4Å: Chain H: N.134, T.136, S.141 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain I: S.284, N.318 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.284 NAG.9: 3 residues within 4Å: Chain K: N.134, T.136, S.141 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain L: S.284, N.318 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.284 NAG.11: 3 residues within 4Å: Chain N: N.134, T.136, S.141 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:T.136 NAG.12: 2 residues within 4Å: Chain O: S.284, N.318 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basore, K. et al., Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor. Nature (2021)

Release Date

2021-10-13

Peptides

Low-density lipoprotein receptor class A domain-containing protein 3: ABCD
E1 envelope glycoprotein: EHKN
E2 envelope glycoprotein: FILO
Capsid: GJMP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
M

C
N

D
P

E
D

H
C

K
B

N
A

F
H

I
G

L
F

O
E

G
L

J
K

M
J

P
I

Low-density lipoprotein receptor class A domain-containing protein 3

E1 envelope glycoprotein

E2 envelope glycoprotein

Capsid

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