SMTL ID : 7s6l.1

J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-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: 6 residues within 4Å: Chain A: N.717, T.719, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.925, A:Q.926 NAG-NAG.2: 6 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103, Y.1110, P.1112 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: N.717, L.922, N.925 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.922, D:N.925 NAG-NAG.4: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain E: N.717, T.719, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.922, E:N.925, E:Q.926 NAG-NAG.6: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain E: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: K.795, N.801, S.803 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: C.1082, C.1126, I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, L.368 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: V.615, N.616, Q.644 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.709, N.710 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain D: F.800, N.801, S.803 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: C.1082, I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain E: N.616, Q.644 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain E: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain E: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain E: C.1082, I.1132, V.1133, N.1134 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: ADE
J08 fragment antigen binding heavy chain variable domain: B
J08 fragment antigen binding light chain variable domain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

B
H

C
L

Spike glycoprotein

J08 fragment antigen binding heavy chain variable domain

J08 fragment antigen binding light chain variable domain

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