SMTL ID : 7wz2.1

SARS-CoV-2 (D614G) Spike trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: E.465 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: G.339, N.343 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.717, L.922 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: Y.28, N.61 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: 5 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: T.716, N.717, L.922, Q.926 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: Q.895 Chain C: E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.709, I.1130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, W. et al., Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer. J.Virol. (2022)

Release Date

2022-07-20

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Spike glycoprotein

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