SMTL ID : 8vkm.1

Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

19 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 No protein-ligand interaction detected (PLIP) 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: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 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 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.918 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 No protein-ligand interaction detected (PLIP) 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: 4 residues within 4Å: Chain A: Q.891 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)

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.20: 5 residues within 4Å: Chain D: 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.21: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.129, N.161 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: T.105, N.230, T.232 Chain C: K.458, E.461 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.276, E.277, N.278 Chain C: K.554 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: H.335, N.339 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.705 Chain B: I.790, Y.792 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: E.129, N.161 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: T.105, N.230, T.232 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: K.554 Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: H.335, N.339 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: S.704, N.705 Chain C: Y.792 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.129, N.161 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain B: R.453, K.458, E.461 Chain C: T.105, N.230, T.232 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.276, E.277, N.278 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.327, P.575, Q.576 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: H.335, N.339 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: Y.792 Chain C: N.705 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition. To Be Published

Release Date

2024-02-14

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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