SMTL ID : 7m6f.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

15 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: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain E: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.717, T.719, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, S.373 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: G.339, N.343, S.373 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.343 NAG-NAG.15: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.122, A.123, N.125 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.122, A.123, N.125 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: E.281, N.282 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: H.655, N.657 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain E: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.122, A.123 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.165, T.167 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: G.232, I.233, N.234 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: N.331, Q.580 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: D.796 Chain E: N.709, I.1130 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.616 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: ABE
BG1-22 Fab Heavy Chain: CF
BG1-22 Fab Light Chain: DG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

C
C

F
H

D
D

G
L

Spike glycoprotein

BG1-22 Fab Heavy Chain

BG1-22 Fab Light Chain

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