SMTL ID : 8hfx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

17 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: 5 residues within 4Å: Chain D: N.53, T.55, E.57, N.58, R.339 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 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: 6 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100, Y.1107, P.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: K.555 Chain C: N.277, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.793 NAG-NAG.14: 2 residues within 4Å: Chain C: N.714, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: G.796, N.798, N.922, N.925 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: S.701, A.703, N.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.703 NAG-NAG.17: 3 residues within 4Å: Chain C: N.1095, T.1097, 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)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 2 residues within 4Å: Chain D: S.544, N.545 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: Q.14, C.15, N.17 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: F.84, D.86, N.231, I.232 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: D.336, N.340, V.364, N.367 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.120, T.122, F.152 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: E.130, N.160 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.231, T.233 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: F.339, N.340 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: A.703, S.708, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.17, N.135 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: C.15, N.17 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain C: N.120, T.122, N.123, V.125, F.152, Y.155 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: A.158, N.159, N.160 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: E.462 Chain C: T.106, I.230, N.231 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: D.336, N.340 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: E.429, N.431 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: E.294, K.295, N.298 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.90, T.92 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.50: 2 residues within 4Å: Chain D: H.373, H.377 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.373, D:H.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, P. et al., Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. J.Virol. (2023)

Release Date

2023-08-30

Peptides

Spike glycoprotein,Envelope glycoprotein: ABC
Angiotensin-converting enzyme: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

Spike glycoprotein,Envelope glycoprotein

Angiotensin-converting enzyme

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