SMTL ID : 8ze6.1

Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

6 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: 6 residues within 4Å: Chain A: L.39, F.40, N.41, N.46, S.47, S.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.48, A:S.48 NAG-NAG.2: 5 residues within 4Å: Chain A: I.155, Q.188, N.190, T.192, E.193 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.282, S.309, S.310, T.311, R.557, D.639 Chain B: H.130 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: E.28, L.39, N.46, S.47, S.48 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: I.155, Q.188, N.190, T.192, E.193, K.228 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain C: H.130 Chain D: I.280, N.282, S.310, T.311, R.557, D.639 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: W.148, N.242 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: E.34, N.36, N.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.34, A:E.34, A:N.36 NAG.10: 4 residues within 4Å: Chain D: E.34, N.35, N.36, N.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.36, D:N.53 NAG.11: 3 residues within 4Å: Chain D: R.108, I.109, N.111 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.111 Water bridges: D:N.111, D:N.111 NAG.12: 3 residues within 4Å: Chain D: W.148, T.240, N.242 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.242

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Y.508, S.591, Y.592, V.617, Y.623, Y.627, V.672 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.508, A:S.591, A:Y.592, A:Y.623

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, M. et al., Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4. To Be Published

Release Date

2024-10-30

Peptides

Dipeptidyl peptidase 4: AD
Spike glycoprotein: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
D

B
A

C
C

Dipeptidyl peptidase 4

Spike glycoprotein