SMTL ID : 8zhd.1

SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-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)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.333, V.357 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: F.328, G.329, F.332, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.707, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1088, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: F.328, G.329, N.333 Chain F: E.76 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.1088, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1124 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.18, N.51 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.112, T.114, V.117 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: Q.105, E.122, N.154, N.155, T.157 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.224 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.271, N.272 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.321, P.569, Q.570, L.572 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.647 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.699 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.696, E.1062, N.1064 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.18, N.51 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: V.110, N.112, T.114, V.117 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.155, T.157 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.224 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.271, N.272 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: P.320, N.321 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: H.645, N.647 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.699 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: A.696, E.1062, N.1064 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: F.49, N.51 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: V.110, N.112, T.114, V.117 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.122, N.155 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: E.455, R.456 Chain C: T.104, N.224 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: K.548 Chain C: E.271, N.272 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.321, Q.570 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: 2 residues within 4Å: Chain A: D.786 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 R1-26 Fab: DF
Light chain of R1-26 Fab: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
F

E
L

G
G

Spike glycoprotein,Fibritin,Expression Tag

Heavy chain of R1-26 Fab

Light chain of R1-26 Fab

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