SMTL ID : 8jyn.1

Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

8 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: 4 residues within 4Å: Chain A: N.712, L.917, Q.921, Q.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.796 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.712, L.917 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.917 NAG-NAG.4: 1 residues within 4Å: Chain B: N.796 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: Q.111, V.126, E.128, N.160, C.161, T.162 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.111 NAG-NAG.6: 3 residues within 4Å: Chain C: N.712, L.917, Q.921 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.917 NAG-NAG.7: 3 residues within 4Å: Chain C: N.796, S.798, Q.799 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)

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.9: 3 residues within 4Å: Chain A: T.410 Chain D: K.8, N.72 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.10: 10 residues within 4Å: Chain D: N.85, H.327, P.328, T.329, A.330, E.357, H.360, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.492, D:Y.492, D:Y.492

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

NAG.11: 2 residues within 4Å: Chain A: Y.24, N.57 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.104, N.229, T.231 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.275, N.277, T.279 Chain B: K.553 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.611, Q.639 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.704 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.701, E.1067, K.1068, N.1069 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.326, Q.575 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: T.104, N.229 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.277 Chain C: K.553 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.611, Q.639 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.704 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.24, N.57 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: G.227, I.228, N.229 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.276, N.277 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.611, T.613 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.650, N.652 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.791 Chain C: N.704 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: Q.890 Chain C: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.304 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain D: N.414 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain D: N.35, E.39, Q.322 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB.1.5 variant. To Be Published

Release Date

2024-01-03

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
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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