SMTL ID : 8xuz.1

Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.786, S.788 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.702, L.907 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.702, L.907 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.907 NAG-NAG.6: 2 residues within 4Å: Chain C: N.702, L.907 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.907 NAG-NAG.7: 2 residues within 4Å: Chain C: N.786, S.788 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: S.402, D.525, S.527, N.528 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.5: 4 residues within 4Å: Chain C: Q.103, N.152, C.153, T.154 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain D: K.8, N.72, T.74 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.9: 5 residues within 4Å: Chain D: K.291, E.294, V.298, P.303, N.304 No protein-ligand interaction detected (PLIP)

1 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.11: 13 residues within 4Å: Chain D: N.85, H.327, P.328, T.329, A.330, H.356, E.357, H.360, N.376, E.384, F.486, Y.492, R.496 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.492, D:Y.492, D:R.496, D:Y.492

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

NAG.12: 3 residues within 4Å: Chain A: N.20, S.50, N.51 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: N.110, T.112, N.113, F.115, E.141 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.96, N.220, T.222 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.266, E.267, N.268, T.270 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.601, T.603 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.694 Chain C: Y.781 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.691, E.1057, K.1058, N.1059 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1119 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: Q.103, V.118, N.152 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.110, T.112, N.113, F.115 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.151, N.152 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.96, N.220, T.222 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.266, E.267, N.268 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.601, T.603 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.642 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.694 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1059 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1119 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: Y.18, T.19, N.20, N.51 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.110, T.112, F.115 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: G.218, N.220 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.266, E.267, N.268 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: Y.640, N.642 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: I.779 Chain C: N.694 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: Q.880 Chain C: E.1057, N.1059 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.601, T.603 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.340, T.342 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.329 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: ABC
Processed angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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