SMTL ID : 7ru1.1

SARS-CoV-2-6P-Mut7 S protein (C3 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

homo-trimer

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: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.7: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: R.457, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.11: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.616, T.618, T.645, R.646 Chain B: I.834 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.709, N.710 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.165 Chain C: Y.351, A.352, I.468 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: N.616, T.618, T.645, R.646 Chain C: I.834 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.709, N.710 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Y.351, A.352, I.468 Chain B: N.165 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: I.834 Chain C: N.616, T.618, T.645, R.646 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: Y.351, A.352, I.468 Chain C: N.165 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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