SMTL ID : 8vcr.1

SARS-CoV-2 Spike S2 bound to Fab 54043-5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 3 residues within 4Å: Chain A: N.131, S.133, Q.134 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain H: N.131, S.133, Q.134 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain I: N.131, S.133, Q.134 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: N.39, G.461 Chain H: D.126 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.47, Q.256, Q.401 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.428, T.430, H.431, F.433 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: C.412, N.464 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: N.31, S.32, Y.34 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain C: N.31, Y.34 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain F: N.31, Y.34 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain H: N.39, G.461 Chain I: D.126 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain H: N.47, Q.256, Q.401 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain H: N.428, T.430, H.431, F.433 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain H: C.412, N.464 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: D.126 Chain I: N.39, G.461 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain I: N.47, Q.256, Q.401 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain I: N.428, T.430, H.431, F.433 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain I: C.412, N.464 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, N.V. et al., Discovery and characterization of a pan-betacoronavirus S2-binding antibody. Structure (2024)

Release Date

2024-07-31

Peptides

Spike protein S2: AHI
54043-5 Fab Heavy Chain: BCF
54043-5 Fab Light Chain: DEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
B

I
C

B
D

C
E

F
H

D
F

E
G

G
L

Spike protein S2

54043-5 Fab Heavy Chain

54043-5 Fab Light Chain