SMTL ID : 8y1f.1

The closed conformation of the HKU1-B S protein in the apo state

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: 6 residues within 4Å: Chain A: D.17, F.18, N.132, T.154, D.177 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN-MAN.6: 6 residues within 4Å: Chain A: I.494 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: 7 residues within 4Å: Chain B: I.494, H.562 Chain C: D.17, F.18, N.132, T.154 Ligands: NAG.50 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: 4 residues within 4Å: Chain A: H.142, I.145, E.147, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.331, N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: D.326, N.355, T.358, N.605 Chain C: Y.528 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.528 NAG-NAG.5: 2 residues within 4Å: Chain A: L.662, N.664 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: I.145, E.147, 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 A: Y.528 Chain B: N.355, T.358, N.605 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.528 NAG-NAG.10: 2 residues within 4Å: Chain B: L.662, N.664 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.145, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: Y.528 Chain C: D.326, N.355, T.358, N.605 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.528 NAG-NAG.15: 2 residues within 4Å: Chain C: L.662, N.664 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: N.19, N.22 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: Y.28, N.29, T.31 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: 2 residues within 4Å: Chain A: I.169, N.171 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.192, S.194 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: S.247, T.249, D.250, N.251 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: 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: 6 residues within 4Å: Chain A: G.617, V.618, C.619, Y.699, N.702, N.703 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: D.714, N.725, T.727 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain A: N.1211 Chain B: D.880, N.881, Q.1001 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.19, N.22 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: Y.28, N.29, T.31 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.58 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: I.169, 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: D.250, N.251 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.433 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.454 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Q.683, N.684 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: G.617, V.618, C.619, N.702, N.703 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: D.714, N.725, T.727 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: 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: 4 residues within 4Å: Chain B: E.920, A.921, N.924, S.929 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: V.1210, N.1211 Chain C: D.880, Q.1001 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.19, N.22 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.11 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: 1 residues within 4Å: Chain C: N.114 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: I.169, N.171 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: N.192, S.194, V.216 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: S.247, D.250, N.251 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: V.432, 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: 5 residues within 4Å: Chain C: G.617, V.618, C.619, N.702, N.703 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain C: F.713, D.714, N.725, T.727 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain C: S.732, 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: 3 residues within 4Å: Chain C: E.920, N.924, S.929 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain A: D.880, N.881, Q.1001 Chain C: 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
A

B
B

C
C

Spike glycoprotein

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