SMTL ID : 8wmd.1

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-2 state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.24, N.57 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: T.104, N.229 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.277 Chain C: K.553 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.611, T.613, Q.639 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: Y.650, V.651, N.652 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.704 Chain B: Y.791 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: A.701, E.1067, N.1069 Chain B: Q.890 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: Y.24, N.57 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: T.104, N.229 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: K.553 Chain B: N.277 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.611, T.613, Q.639 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: Y.650, V.651, N.652 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.704 Chain C: Y.791 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: A.701, E.1067, N.1069 Chain C: Q.890 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: Y.24, N.57 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.159, N.160 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: T.104, N.229 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: K.553 Chain C: N.277 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.611, T.613, Q.639 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: Y.650, V.651, N.652 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: Y.791 Chain C: N.704 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: Q.890 Chain C: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomai, T. et al., Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant. Biorxiv (2024)

Release Date

2024-04-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Spike glycoprotein

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