SMTL ID : 8y1c.1

2up-1 conformation of HKU1-B S protein after incubation of the receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG-MAN-MAN-MAN-MAN.1: 5 residues within 4Å: Chain A: D.17, F.18, N.132, T.154 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN-MAN.6: 5 residues within 4Å: Chain B: D.17, F.18, N.132, T.154 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN-MAN.11: 5 residues within 4Å: Chain B: I.494 Chain C: D.17, F.18, N.132, T.154 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: I.145, K.186, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain A: N.355, S.357, T.358, R.361, N.605, D.606, L.607, L.608, Y.609 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.609 NAG-NAG.5: 2 residues within 4Å: Chain A: L.662, N.664 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: K.186, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: D.326, N.355, T.358, N.605 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: L.662, N.664 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: H.142, I.145, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.331, N.335, V.336, S.337 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain C: P.322, D.326, N.355, T.358, L.608, Y.609 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.643, L.662, N.664 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.643

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

NAG.16: 5 residues within 4Å: Chain A: N.19, N.22 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.29 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.58, E.272 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: V.113, N.114 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: I.169, R.170, N.171 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.192, S.194 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: D.250, N.251 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: V.432, N.433 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.454 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Q.683, N.684 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: G.617, Y.699, N.702, N.703 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: F.713, D.714, N.725, T.727 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: S.732, N.771 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.776 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.793 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: E.920, A.921, N.924, S.929 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: N.1211 Chain B: D.880, N.881, S.980, Q.1001 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain B: N.19, C.20, T.21, N.22 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.6, NAG-NAG-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: Y.28, N.29, K.30 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.58, E.272 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: V.113, N.114 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.171 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.192, S.194 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: S.247, N.251 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: P.430, V.432, N.433 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.454 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.684 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain B: G.617, V.618, C.619, I.632, Y.699, N.703 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: F.713, D.714, N.725, T.727 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: S.732, N.771 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.776 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.793 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: E.920, N.924 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: N.1211 Chain C: D.880, N.881, Q.1001 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.19, N.22 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: Y.28, N.29 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.58, E.272 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: V.113, N.114 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.171 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: N.192, S.194, A.195 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: T.249, D.250, N.251 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.433 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain C: N.454 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: Q.683, N.684 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain C: G.617, V.618, N.702, N.703 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain C: D.714, N.725, T.727, S.728 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain C: P.769, N.771 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.776 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain C: N.793 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain C: N.924, S.929 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain A: D.880 Chain C: T.781, N.1211 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, L. et al., Structural basis for the recognition of HCoV-HKU1 by human TMPRSS2. Cell Res. (2024)

Release Date

2024-05-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Spike glycoprotein

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