SMTL ID : 8zhm.1

SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs

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.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1088, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1124 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Y.18, N.51 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Q.105, E.122, N.155, T.157 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.224 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.271, N.272 Chain C: K.548 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.321, I.322, Q.570, T.571 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: F.332, N.333 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.647 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.699 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: A.696, E.1062, K.1063, N.1064 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.18, N.51 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: V.110, N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: E.122, N.155, T.157 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.224 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.271, N.272 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.321, I.322, P.569, Q.570 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.333, F.364 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.647 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.699 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.696, E.1062, N.1064 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.51 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain C: V.110, N.112, T.114, N.115, V.117, F.147 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: Q.105, N.154, N.155, T.157 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.224 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: K.548 Chain C: E.271, N.272 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.321, Q.570 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.333 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.606 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: H.645, N.647 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.699 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1064 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Q. et al., Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun (2024)

Release Date

2024-08-21

Peptides

Spike glycoprotein,Fibritin,Expression Tag: ABC
Heavy chain of R1-32 Fab: DFH
Light chain of R1-32 Fab: EGI
Light chain of H18 Fab: JLN
Heavy chain of H18 Fab: KMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
G

H
N

E
L

G
I

I
O

J
D

L
F

N
K

K
E

M
J

O
M

Spike glycoprotein,Fibritin,Expression Tag

Heavy chain of R1-32 Fab

Light chain of R1-32 Fab

Light chain of H18 Fab

Heavy chain of H18 Fab

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