SMTL ID : 8hc4.1

SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-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: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 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: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.30, N.61 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: V.120, N.122, T.124, V.159 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.165 Chain O: S.69 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: V.120, N.122, T.124, V.127, F.157 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.164, N.165 Chain E: S.69 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.122, T.124, E.154, F.157 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.164, N.165, T.167 Chain K: S.74 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: K.557, K.558 Chain C: N.282 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: Q.895 Chain C: A.706, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants. Nat Commun (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: ABC
Heavy chain of R1-32 Fab: DJN
Light chain of R1-32 Fab: EKO
Heavy chain of YB9-258: FHL
Light chain of YB9-258 Fab: GIM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

J
K

N
N

E
E

K
M

O
O

F
F

H
H

L
G

G
J

I
L

M
I

Spike glycoprotein

Heavy chain of R1-32 Fab

Light chain of R1-32 Fab

Heavy chain of YB9-258

Light chain of YB9-258 Fab

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