SMTL ID : 7y71.1

SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

7 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: 2 residues within 4Å: Chain C: N.316, Q.565 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: N.1083, T.1085, H.1086, F.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: A.691, E.1057, K.1058, N.1059 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain E: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain E: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain E: A.691, N.1059 No protein-ligand interaction detected (PLIP)

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

NAG.8: 1 residues within 4Å: Chain C: N.694 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain D: N.265, N.267 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.265, D:E.266, D:E.266 NAG.10: 2 residues within 4Å: Chain D: N.601, T.603 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.603 NAG.11: 2 residues within 4Å: Chain D: H.640, N.642 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.642 NAG.12: 3 residues within 4Å: Chain D: N.694, G.1116 Chain E: D.781 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.694 NAG.13: 1 residues within 4Å: Chain D: N.702 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.702 NAG.14: 3 residues within 4Å: Chain D: N.1083, H.1086, F.1088 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.1083, D:N.1083, D:H.1086 NAG.15: 1 residues within 4Å: Chain D: N.1119 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.1119, D:N.1119 NAG.16: 2 residues within 4Å: Chain E: N.265, N.267 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.265 NAG.17: 2 residues within 4Å: Chain E: N.601, T.603 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain E: H.640, N.642 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain E: N.694, G.1116 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.694 NAG.20: 2 residues within 4Å: Chain E: N.1083, H.1086 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.1083, E:H.1086 NAG.21: 1 residues within 4Å: Chain E: N.1119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.1119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chia, W.N. et al., Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. Sci Adv (2023)

Release Date

2023-08-02

Peptides

Fab E7 light chain: A
Fab E7 heavy chain: B
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
O

C
A

D
B

E
C

Fab E7 light chain

Fab E7 heavy chain

Spike glycoprotein

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