SMTL ID : 8dm9.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

18 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: C.15, N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.15, N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.15: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: N.120, A.121, T.122, N.123, V.125 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: E.130, N.159, N.160 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.231 Chain C: K.459, E.462 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, V.364, L.368, F.371 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.120, T.122, V.125, F.152 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: E.130, N.159, N.160 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: T.106, N.231, T.233 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain B: L.458, K.459, E.462 Chain C: T.106, N.231, T.233 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.120, T.122, V.125, F.152 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: E.130, N.159, N.160 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: K.555 Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: D.336, N.340 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: N.53, R.340 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain D: N.546 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-02-08

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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