SMTL ID : 7m6h.1

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG7-20

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: V.120, N.122, N.125, V.127 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: E.465 Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.616, T.618, R.646 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.717, Q.1071 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.122, N.125, V.127 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: T.114, N.234 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: D.614, V.615, N.616 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: D.796 Chain C: S.708, N.709, N.710 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.717, F.718, Q.1071 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 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
BG7-20 Fab Heavy Chain: DE
BG7-20 Fab Light Chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Spike glycoprotein

BG7-20 Fab Heavy Chain

BG7-20 Fab Light Chain

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