SMTL ID : 8vkl.1

Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

20 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 A: N.119, T.121, N.122, V.124, E.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.122 NAG-NAG.2: 4 residues within 4Å: Chain A: N.713, L.918, Q.922, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: A.702, E.1068, N.1070 Chain B: Q.891 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.119, T.121, N.122, V.124, E.150 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.713, L.918, Q.922, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: A.702, E.1068, N.1070 Chain C: Q.891 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.119, T.121, N.122, V.124, E.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.122 NAG-NAG.14: 4 residues within 4Å: Chain C: N.713, L.918, Q.922, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.702, E.1068, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain D: N.53, T.55, E.57, N.58, R.340 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: N.53, T.55, E.57, N.58, R.340 No protein-ligand interaction detected (PLIP)

2 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.20: 5 residues within 4Å: Chain D: K.416, S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain E: K.416, S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: E.129, N.161 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: T.105, N.230, T.232 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.276, E.277, N.278 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: H.335, N.339 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.705 Chain B: I.790, Y.792 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.129, N.161 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: T.105, N.230, T.232 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: K.554 Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: H.335, N.339 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: S.704, N.705 Chain C: Y.792 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.129, N.161 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: K.458, E.461 Chain C: T.105, N.230, T.232 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.276, E.277, N.278 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: H.335, N.339 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: I.790, Y.792 Chain C: N.705 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein. Nat Commun (2024)

Release Date

2024-02-14

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

Spike glycoprotein

Angiotensin-converting enzyme 2

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