SMTL ID : 7e5r.1

SARS-CoV-2 S trimer with three-antibody cocktail complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-3-3-3-3-3-3-3-mer

Ligands

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain G: N.87, N.234, T.236 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:N.87 Hydrogen bonds: G:N.87 NAG-NAG.2: 5 residues within 4Å: Chain G: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:L.922, G:N.925, G:Q.926 Hydrogen bonds: G:N.925 NAG-NAG.3: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain G: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain G: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain N: N.87, N.234, T.236 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:N.87 Hydrogen bonds: N:N.87 NAG-NAG.7: 5 residues within 4Å: Chain N: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:L.922, N:N.925, N:Q.926 Hydrogen bonds: N:N.925 NAG-NAG.8: 3 residues within 4Å: Chain N: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain N: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain N: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain U: N.87, D.88, N.234, T.236 1 PLIP interactions: 1 interactions with chain U Hydrophobic interactions: U:N.87 NAG-NAG.12: 5 residues within 4Å: Chain U: N.717, L.922, N.925, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain U Hydrophobic interactions: U:L.922, U:Q.926 Hydrogen bonds: U:N.925 NAG-NAG.13: 3 residues within 4Å: Chain U: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain U: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain U: N.1134 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Y. et al., Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms. Cell Res. (2021)

Release Date

2021-10-13

Peptides

H014 light chain: ACE
H014 heavy chain: BDF
Spike glycoprotein: GNU
P17 heavy chain: HJL
P17 light chain: IKM
FC05 light chain: OQS
FC05 heavy chain: PRT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
D

E
E

B
L

D
N

F
O

G
A

N
B

U
C

H
M

J
T

L
I

I
U

K
V

M
K

O
R

Q
S

S
Q

P
W

R
X

T
P

H014 light chain

H014 heavy chain

Spike glycoprotein

P17 heavy chain

P17 light chain

FC05 light chain

FC05 heavy chain

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