SMTL ID : 8zdx.1

Crystal structure of MjHKU4r-CoV-1 RBD bound to hDPP4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

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.1: 6 residues within 4Å: Chain A: I.157, Q.190, N.192, T.194, E.195, K.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.195 NAG-NAG-BMA.2: 6 residues within 4Å: Chain B: N.182, T.184, Q.271, E.272, Y.293, E.295 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 5 residues within 4Å: Chain B: I.157, N.192, T.194, E.195 Chain C: E.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.194 NAG-NAG.4: 3 residues within 4Å: Chain B: W.150, V.242, N.244 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.150 NAG-NAG.5: 5 residues within 4Å: Chain B: R.280, I.282, N.284, R.559 Chain C: H.129 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: N.43, N.48, S.49, S.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.43, A:N.48, A:S.50 NAG.7: 1 residues within 4Å: Chain A: N.113 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: N.182, T.184, Q.271, E.272 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.184 Hydrogen bonds: A:Q.271 NAG.9: 5 residues within 4Å: Chain B: V.41, N.43, N.48, S.49, S.50 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: N.30, K.33, M.207 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.33 NAG.12: 3 residues within 4Å: Chain D: N.30, T.32, K.33 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.32, D:K.33

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 6 residues within 4Å: Chain B: R.24, K.34, D.67, Y.68, S.69, I.70 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.34, B:K.34, B:Y.68, B:I.70 Salt bridges: B:R.24, B:D.67, B:D.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, M. et al., Structural basis for human DPP4 receptor recognition by a pangolin MERS-like coronavirus. Plos Pathog. (2024)

Release Date

2024-10-30

Peptides

Dipeptidyl peptidase 4 membrane form: AB
Spike glycoprotein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Dipeptidyl peptidase 4 membrane form

Spike glycoprotein

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