SMTL ID : 7m6e.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG10-19

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 7 residues within 4Å: Chain B: L.335, E.340, N.343 Chain E: Q.100, Y.105, F.109, Y.111 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.335

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

NAG.2: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.280, N.282 Chain D: K.558 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.12: 7 residues within 4Å: Chain A: G.339, E.340, N.343 Chain F: Q.100, N.104, F.109, Y.111 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain D: D.796 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: A.706, N.1074 Chain D: Q.895 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain C: Q.100, F.109, Y.111 Chain D: E.340, N.343 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.165 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: T.108, N.234, T.236 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: K.558 Chain D: N.280, N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.616, Q.644 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: D.796 Chain D: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: Q.895 Chain D: A.706, N.1074 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: ABD
BG10-19 Fab Heavy Chain: CEF
BG10-19 Fab Light Chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
E

C
D

E
F

F
H

G
C

H
G

I
L

Spike glycoprotein

BG10-19 Fab Heavy Chain

BG10-19 Fab Light Chain

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