SMTL ID : 7m6i.1

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG1-24

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-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: 2 residues within 4Å: Chain A: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: E.132, N.165 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 3 residues within 4Å: Chain B: E.132, N.165 Chain D: T.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.71, D:T.71

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 3 residues within 4Å: Chain B: D.796 Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP)

26 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.6: 3 residues within 4Å: Chain A: A.27, Y.28, N.61 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: T.307, V.308, E.309, N.603 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.122, N.125 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.19: 10 residues within 4Å: Chain B: K.378, C.379, Y.380, G.381, V.382, F.429, T.430, G.431, C.432, F.515 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scheid, J.F. et al., B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell (2021)

Release Date

2021-05-05

Peptides

Spike glycoprotein: ABC
BG1-24 Fab Heavy Chain: DF
BG1-24 Fab Light Chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

E
L

G
N

Spike glycoprotein

BG1-24 Fab Heavy Chain

BG1-24 Fab Light Chain

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