SMTL ID : 8jyo.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

9 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: 3 residues within 4Å: Chain A: N.712, L.917, Q.921 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.796, S.798 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: 2 residues within 4Å: Chain B: N.796, S.798 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: Q.111, E.128, N.160, C.161 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.712, L.917, Q.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.796, S.798 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) NAG-NAG.11: 4 residues within 4Å: Chain E: 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.9: 3 residues within 4Å: Chain B: T.410 Chain D: K.8, N.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain A: T.410 Chain E: K.8, N.72 No protein-ligand interaction detected (PLIP)

2 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: 11 residues within 4Å: Chain D: N.85, H.327, P.328, T.329, A.330, E.357, H.360, H.383, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.492 NAG-NAG-BMA-MAN-MAN.13: 10 residues within 4Å: Chain E: N.85, H.327, T.329, A.330, E.357, H.360, H.383, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.492

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

NAG.14: 1 residues within 4Å: Chain A: N.57 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.118, A.119, T.120, V.123 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: Q.111, N.159, N.160 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: G.227, I.228, N.229 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.275, E.276, N.277, T.279 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.611 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.704 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.1093, T.1095, H.1096 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.326, Q.575 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.338 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.118, T.120, V.123 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: K.109, E.128, N.159, N.160 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: T.104, N.229, T.231 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.276, N.277 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.611, Q.639 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: I.789, Y.791 Chain B: N.704 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.1067, N.1069 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.1093, H.1096 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.326, Q.575 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.338, T.340 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.24, N.57 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.118, A.119, T.120, N.121, V.123 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.229 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: K.553 Chain C: N.275, E.276, N.277 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.611, T.613, E.614, Q.639 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.650, N.652 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: I.789 Chain C: N.704 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.701, E.1067, K.1068, N.1069 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.1093, H.1096 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.326, Q.575 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain D: N.304 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain D: N.414 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: N.35, E.39, Q.322 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.304 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain E: N.414 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: 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 Omicron XBB.1.5 variant. Nat Commun (2024)

Release Date

2024-01-03

Peptides

Spike glycoprotein: ABC
Processed angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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