SMTL ID : 7e5s.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-3-2-2-2-2-3-1-3-1-mer

Ligands

12 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: 5 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.926 Hydrogen bonds: A:Q.926 NAG-NAG.2: 4 residues within 4Å: Chain A: N.801, S.803, Q.804, N.928 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.926 Hydrogen bonds: B:Q.926 NAG-NAG.5: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: G.1085, C.1126, D.1127, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.87, D.88, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.717, L.922, Q.926, A.1070, Q.1071 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.926 Hydrogen bonds: C:Q.926 NAG-NAG.10: 3 residues within 4Å: Chain C: K.795, G.799, N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: F.1075, N.1098, Y.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: G.1085, C.1126, D.1127, 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

2021-11-17

Peptides

Spike glycoprotein: ABC
H014 light chain: DF
H014 heavy chain: EJ
P17 heavy chain: GH
P17 light chain: IQ
FC05 light chain: KNP
HB27 light chain: L
FC05 heavy chain: MRS
HB27 heavy chain: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

E
E

J
L

G
I

H
J

I
K

Q
T

K
N

N
Q

P
S

L
O

M
P

R
U

S
V

O
R

Spike glycoprotein

H014 light chain

H014 heavy chain

P17 heavy chain

P17 light chain

FC05 light chain

HB27 light chain

FC05 heavy chain

HB27 heavy chain

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