SMTL ID : 8v06.1 (1 other biounit)

Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-dimer

Ligands

1 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: 9 residues within 4Å: Chain A: E.61, A.62, V.63, P.82, Y.212, N.261, G.432, Q.436 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.212

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.2: 4 residues within 4Å: Chain B: E.61, Y.212, N.213 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 11 residues within 4Å: Chain B: E.61, A.62, V.63, S.80, P.82, Q.86, N.261, G.432, L.433, Q.436 Ligands: NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.86

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

NAG.4: 4 residues within 4Å: Chain A: E.61, Y.212, N.213 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.212 Hydrogen bonds: A:E.61 NAG.5: 2 residues within 4Å: Chain B: N.76, A.77 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain B: F.104, H.178, K.180, N.195, M.304, H.393, K.395, N.409 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.195, B:N.409, B:Y.414 Salt bridges: B:H.178, B:K.180, B:H.393, B:K.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, M. et al., Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4. Structure (2024)

Release Date

2024-03-13

Peptides

5'-3' exonuclease PLD3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-3' exonuclease PLD3

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