SMTL ID : 8v5t.2 (1 other biounit)

Crystal structure of Alzheimers disease phospholipase D3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 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: 5 residues within 4Å: Chain A: E.82, Y.235, N.236 Ligands: NAG-NAG.2, SO4.6 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 11 residues within 4Å: Chain A: E.82, A.83, V.84, G.101, N.102, P.103, N.284, G.455, L.456, Q.459 Ligands: NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: F.125, H.201, K.203, N.218, H.416, K.418 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.218 Salt bridges: A:H.201, A:K.203, A:H.416, A:K.418 SO4.4: 3 residues within 4Å: Chain A: K.194, A.257, G.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.258 Salt bridges: A:K.194 SO4.5: 8 residues within 4Å: Chain A: N.274, E.276, S.302, G.303, R.304, T.305, P.306, K.309 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.276, A:R.304 Water bridges: A:N.274 Salt bridges: A:K.309 SO4.6: 3 residues within 4Å: Chain A: G.111, H.211 Ligands: NAG-NAG.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.115, A:G.115 Salt bridges: A:H.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishii, K. et al., Crystal structure of Alzheimer's disease phospholipase D3 provides a molecular basis for understanding its normal and pathological functions. Febs J. (2024)

Release Date

2024-10-09

Peptides

5'-3' exonuclease PLD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

5'-3' exonuclease PLD3

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