SMTL ID : 8xvm.1

Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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: 1 residues within 4Å: Chain A: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.786, S.788 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: N.786, S.788 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 1 residues within 4Å: Chain E: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 2 residues within 4Å: Chain E: N.786, S.788 No protein-ligand interaction detected (PLIP)

3 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.3: 2 residues within 4Å: Chain A: T.401 Chain B: N.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain C: T.401 Chain D: N.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 2 residues within 4Å: Chain E: T.401 Chain F: N.72 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 15 residues within 4Å: Chain B: N.85, H.327, P.328, T.329, A.330, H.356, E.357, H.360, D.364, N.376, H.383, E.384, F.486, Y.492, R.496 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.496, B:Y.492, B:Y.492 NAG-NAG-BMA-MAN-MAN.23: 15 residues within 4Å: Chain D: N.85, H.327, P.328, T.329, A.330, H.356, E.357, H.360, D.364, N.376, H.383, E.384, F.486, Y.492, R.496 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.496, D:Y.492, D:Y.492 NAG-NAG-BMA-MAN-MAN.42: 15 residues within 4Å: Chain F: N.85, H.327, P.328, T.329, A.330, H.356, E.357, H.360, D.364, N.376, H.383, E.384, F.486, Y.492, R.496 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.496, F:Y.492, F:Y.492

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

NAG.5: 2 residues within 4Å: Chain A: Y.18, N.51 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.110, T.112, F.115 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: E.120, N.151, N.152 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: T.96, N.220, T.222 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.266, E.267, N.268, T.270 Chain E: K.543 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.601, T.603 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: S.693, N.694 Chain C: I.779 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: A.691, E.1057, N.1059 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.1083, H.1086, F.1088 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1119 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.317, Q.565 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: V.298, N.304 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.414, W.576 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.35, E.39, Q.322 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: Y.18, N.51 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.110, T.112, F.115 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: E.120, N.151, N.152 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: T.96, N.220, T.222 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: K.543 Chain C: N.266, E.267, N.268, T.270 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.601, T.603 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: S.693, N.694 Chain E: I.779 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: A.691, E.1057, N.1059 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.1083, H.1086, F.1088 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1119 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.317, Q.565 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: V.298, N.304 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.414, W.576 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: N.35, E.39, Q.322 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: Y.18, N.51 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.110, T.112, F.115 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: E.120, N.151, N.152 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: T.96, N.220, T.222 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: K.543 Chain E: N.266, E.267, N.268, T.270 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.601, T.603 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain E: N.642 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain A: I.779 Chain E: S.693, N.694 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: A.691, E.1057, N.1059 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.1083, H.1086, F.1088 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.1119 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.317, Q.565 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain F: V.298, N.304 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.414, W.576 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain F: N.35, E.39, Q.322 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yajima, H. et al., Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nat Commun (2024)

Release Date

2024-10-09

Peptides

Spike glycoprotein: ACE
Processed angiotensin-converting enzyme 2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
D

D
D

F
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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