SMTL ID : 8ify.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

14 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.313, I.314, Q.562 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.691 Chain B: Y.778 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.778 NAG-NAG.3: 4 residues within 4Å: Chain A: N.699, L.904, Q.908, Q.1053 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.783, S.785 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1080, T.1082, H.1083, F.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: I.1114, V.1115, N.1116 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.699, L.904, Q.908, Q.1053 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.783, S.785, Q.786 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1080, T.1082, H.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1116 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.699, L.904 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.783, S.785, Q.786 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.1080, T.1082, H.1083, F.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.1116 No protein-ligand interaction detected (PLIP)

25 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.15: 2 residues within 4Å: Chain A: E.263, N.264 Ligand excluded by PLIP NAG.16: 7 residues within 4Å: Chain A: F.320, D.321, F.324, N.325, V.349, N.352, N.419 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.585 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.598 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1056 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.12, N.45 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.263, N.264 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.598 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.691 Chain C: Y.778 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.1054, N.1056 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.12, N.45 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.262, N.264 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.313, Q.562 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.598, T.600 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: Y.778 Chain C: N.691 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: E.1054, N.1056 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: T.34, N.35, K.322 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: N.413, E.414, I.417, W.575 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain D: K.277, N.280, Q.281, G.403, L.404, E.406 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: D.524, N.527 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.35, T.37, N.40 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.413 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: K.277, N.280, Q.281 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.527 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.72, T.74 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.41: 3 residues within 4Å: Chain E: W.459, D.480, P.481 No protein-ligand interaction detected (PLIP)

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: ABC
Angiotensin-converting enzyme: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

Spike glycoprotein

Angiotensin-converting enzyme

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