SMTL ID : 7s6k.1

J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 2)

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.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: C.1082, H.1083, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.922 NAG-NAG.6: 2 residues within 4Å: Chain D: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: C.1082, H.1083, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.922 NAG-NAG.10: 2 residues within 4Å: Chain G: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain G: C.1082, H.1083, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: G.339, N.343, S.373 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: C.15, V.16, N.17 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: N.616, Q.644 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: G.339, N.343, S.373 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: C.15, V.16, N.17 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain G: N.616, Q.644 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: G.339, N.343, S.373 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: C.15, V.16, N.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torres, J.L. et al., Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-11

Peptides

Spike glycoprotein: ADG
J08 fragment antigen binding heavy chain variable domain: BEH
J08 fragment antigen binding light chain variable domain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

Spike glycoprotein

J08 fragment antigen binding heavy chain variable domain

J08 fragment antigen binding light chain variable domain

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