SMTL ID : 7ru5.1

CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

10 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: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.5: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: S.704, C.705, A.706, E.1072, K.1073, N.1074 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.706 Hydrogen bonds: B:S.704 NAG-NAG.7: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.9: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: N.17, C.136, N.137 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: Y.144, H.146, N.148, N.149 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: V.615, N.616, Q.644 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: V.615, N.616, Q.644 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain A: I.834, K.835, Q.836, Y.837 Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain A: Q.895 Chain C: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, F. et al., Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways. Iscience (2022)

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABC
CC6.30 Fab heavy chain Fv: DF
CC6.30 Fab kappa chain Fv: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
H

F
D

E
L

G
E

Spike glycoprotein

CC6.30 Fab heavy chain Fv

CC6.30 Fab kappa chain Fv

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