SMTL ID : 9jcy.1

Crystal structure of the HCoV-HKU1 RBD in complex with Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: D.4, N.33, N.285, S.288 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: N.148, S.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.148 Water bridges: A:T.150

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.83, S.84, Q.88, S.89, K.93, L.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.93, A:K.93 Water bridges: A:V.218 GOL.4: 5 residues within 4Å: Chain A: R.125, Y.126, P.174, S.244, C.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.245, A:C.245 GOL.5: 11 residues within 4Å: Chain B: F.177, P.178, V.180, S.188, L.189, S.190 Chain C: Q.160, S.162, S.176, S.177, T.178 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:F.177, B:S.188, B:S.190, C:Q.160, C:T.178 GOL.6: 2 residues within 4Å: Chain C: N.152, A.153 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies. Nat Commun (2025)

Release Date

2025-07-30

Peptides

Spike protein S1: A
Heavy chain of Fab: B
Light chain of Fab: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Spike protein S1

Heavy chain of Fab

Light chain of Fab

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