SMTL ID : 7r40.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.1085, T.1087, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.1085, T.1087, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain D: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.1085, T.1087, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain G: N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain G: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain G: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP)

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

NAG.13: 5 residues within 4Å: Chain A: N.109, T.111, V.114, K.116, E.141 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.267, E.268, N.269 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: A.693, N.1061 Chain G: Q.882 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: C.2, N.4, N.124 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.318, T.320, Q.567 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: F.329, N.330, F.361 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain D: N.109, T.111, V.114, K.116, E.141 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.267, E.268, N.269 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: H.642, N.644 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Q.882 Chain D: A.693, N.1061 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: C.2, N.4, N.124 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: N.318, T.320, Q.567 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: F.329, N.330, F.361 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain G: N.109, T.111, V.114, K.116, E.141 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: N.267, E.268, N.269 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain G: H.642, N.644 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: Q.882 Chain G: A.693, N.1061 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: C.2, N.4, N.124 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.318, T.320, Q.567 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain G: F.329, N.330, F.361 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, W. et al., An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern. Sci Immunol (2022)

Release Date

2022-04-20

Peptides

Spike glycoprotein: ADG
87G7 light chain variable region: BEH
87G7 heavy chain variable region: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
L

E
F

H
G

C
H

F
D

I
E

Spike glycoprotein

87G7 light chain variable region

87G7 heavy chain variable region

Related Entries With Identical Sequence