SMTL ID : 8q1k.1

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.51 Å
Oligo State
homo-dimer
Ligands
1 x NAG- NAG- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
8 x PO4: PHOSPHATE ION(Non-functional Binders)
4 x MN: MANGANESE (II) ION(Non-covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Roske, Y. et al., Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res. (2024)
Release Date
2023-12-06
Peptides
5'-3' exonuclease PLD3: AB
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B

5'-3' exonuclease PLD3