SMTL ID : 7m6g.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

11 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.331, I.332, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: F.342, N.343, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: S.704, A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP)

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

NAG.12: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: T.307, N.603 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.122, F.157 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.280, N.282, T.284 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.280, N.282, T.284 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: F.338, F.342, N.343, L.368 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1098 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1134 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
BG7-15 Fab Heavy Chain: DE
BG7-15 Fab Light Chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
R

F
L

G
S

Spike glycoprotein

BG7-15 Fab Heavy Chain

BG7-15 Fab Light Chain

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