SMTL ID : 9h0b.1

Crystal structure of the Porcine Hemagglutinating Encephalomyelitis Virus (PHEV) receptor binding domain in complex with porcine DPEP1.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-2-mer

Ligands

4 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: Q.36, N.41, S.43, Y.96 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: K.261, A.262, N.263, Q.266 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 4 residues within 4Å: Chain C: Q.36, N.41, A.95, Y.96 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 4 residues within 4Å: Chain C: K.261, A.262, N.263, Q.266 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.266

16 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: E.350 Chain C: Q.34 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.350, H2O.14 ZN.6: 1 residues within 4Å: Chain A: H.343 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.343 ZN.7: 3 residues within 4Å: Chain A: Q.34, D.37 Chain C: E.350 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.350, H2O.7 ZN.8: 1 residues within 4Å: Chain A: H.47 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.47 ZN.9: 1 residues within 4Å: Chain A: H.178 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.178 ZN.10: 5 residues within 4Å: Chain A: H.20, D.22, E.125, D.288 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.20, A:D.22, A:E.125, A:E.125 ZN.11: 6 residues within 4Å: Chain A: H.20, E.125, H.198, H.219, R.230 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.125, A:H.198, A:H.219, H2O.7 ZN.12: 2 residues within 4Å: Chain A: H.142 Chain C: H.142 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.142, A:H.142 ZN.13: 1 residues within 4Å: Chain A: H.273 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.273, H2O.8 ZN.16: 1 residues within 4Å: Chain C: H.343 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.343 ZN.17: 1 residues within 4Å: Chain C: H.178 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.178 ZN.18: 1 residues within 4Å: Chain C: H.47 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.47 ZN.19: 6 residues within 4Å: Chain C: H.20, D.22, S.66, E.125, D.288 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.20, C:D.22, C:E.125 ZN.20: 6 residues within 4Å: Chain C: H.20, E.125, H.198, H.219, R.230 Ligands: ZN.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.125, C:H.198, C:H.219, H2O.17 ZN.23: 2 residues within 4Å: Chain D: H.139, L.253 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.139 ZN.24: 1 residues within 4Å: Chain D: D.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.6

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

NAG.14: 2 residues within 4Å: Chain B: A.110, N.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.111 NAG.15: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain D: K.14, A.110, N.111 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain D: N.130 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dufloo, J. et al., DPEP1 is the cell receptor of thePorcine Hemagglutinanting Encephalomyelitis Virus. To Be Published

Release Date

2025-08-06

Peptides

Dipeptidase 1: AC
Spike glycoprotein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
C

B
A

D
D

Dipeptidase 1

Spike glycoprotein