SMTL ID : 7cwt.1

SARS-CoV-2 Spike protein in complex with hb27 and fc05 Fab cocktail

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.603, Q.631, T.632 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.631 NAG.2: 5 residues within 4Å: Chain A: A.693, S.698, E.1059, N.1061 Chain C: Q.882 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.698 NAG.3: 4 residues within 4Å: Chain A: K.782, N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG.4: 10 residues within 4Å: Chain A: F.1062, V.1083, S.1084, N.1085, G.1086, T.1087, H.1088, F.1090, Y.1097, P.1099 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1062, A:N.1085, A:F.1090 Hydrogen bonds: A:S.1084, A:N.1085, A:H.1088, A:H.1088 NAG.5: 6 residues within 4Å: Chain A: T.703, N.704, F.705, N.906, L.909, F.1096 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1096 Hydrogen bonds: A:N.704 NAG.6: 4 residues within 4Å: Chain B: N.603, C.604, T.605, Q.631 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.604, B:C.604 NAG.7: 5 residues within 4Å: Chain B: K.782, N.788, F.789, S.790, Q.791 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.788, B:F.789, B:S.790 NAG.8: 5 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090, I.1101 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.1087 Hydrogen bonds: B:N.1085, B:T.1087 NAG.9: 8 residues within 4Å: Chain C: T.703, N.704, F.705, N.906, L.909, Q.913, Q.1058, F.1096 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.705, C:F.1096 Hydrogen bonds: C:Q.913 NAG.10: 5 residues within 4Å: Chain C: K.782, N.788, F.789, S.790, Q.791 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.782 Hydrogen bonds: C:N.788 NAG.11: 6 residues within 4Å: Chain B: Q.882 Chain C: A.693, A.700, E.1059, K.1060, N.1061 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.700, C:E.1059 Hydrogen bonds: C:N.1061, B:Q.882 NAG.12: 7 residues within 4Å: Chain C: F.325, G.326, F.329, N.330, L.355, S.358, S.360 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.329, C:L.355 Hydrogen bonds: C:S.358 NAG.13: 3 residues within 4Å: Chain C: N.644, N.645, Y.647 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.644 NAG.14: 2 residues within 4Å: Chain C: N.603, Q.631 No protein-ligand interaction detected (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

2021-06-23

Peptides

Spike glycoprotein: ABC
Light chain Fab of HB27: DFJ
Heavy chain Fab of HB27: EGI
Light chain Fab of FC05: HKM
Heavy chain Fab of FC05: LNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

J
J

E
E

G
G

I
I

H
H

K
K

M
M

L
L

N
N

O
P

Spike glycoprotein

Light chain Fab of HB27

Heavy chain Fab of HB27

Light chain Fab of FC05

Heavy chain Fab of FC05

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