SMTL ID : 7cwu.1

SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktail

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain G: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain H: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain I: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain I: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain I: N.1098, G.1099, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain I: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain G: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.922 NAG-NAG.8: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain G: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain H: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain H: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain H: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain H: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain I: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain G: H.655, V.656, N.657 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain G: N.709, G.1131 Chain I: D.796 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain H: N.61 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain H: N.603, T.604 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain H: N.616 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain H: H.655, V.656, N.657 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: D.796 Chain H: N.709, G.1131 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain H: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain I: N.603, T.604 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain I: N.616 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain I: H.655, V.656, N.657 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain H: D.796 Chain I: N.709, G.1131 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain I: A.706, E.1072, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Structure-based development of human antibody cocktails against SARS-CoV-2. Cell Res. (2021)

Release Date

2020-12-16

Peptides

heavy chain of FC05 Fab: ACE
light chain of FC05 Fab: BDF
Spike glycoprotein: GHI
heavy chain of P17 Fab: JLN
light chain of P17 Fab: KMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

C
N

E
J

B
I

D
G

F
F

G
B

H
C

I
A

J
H

L
M

N
O

K
L

M
R

O
S

heavy chain of FC05 Fab

light chain of FC05 Fab

Spike glycoprotein

heavy chain of P17 Fab

light chain of P17 Fab

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