SMTL ID : 8v5t.1 (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, GOL.10 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: E.82, A.83, V.84, P.103, N.284, G.455, Q.459 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

6 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.218 Water bridges: A:H.416, A:K.418 Salt bridges: A:H.201, A:K.203, A:H.416, A:K.418 SO4.4: 1 residues within 4Å: Chain A: R.272 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.272 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:S.302 Water bridges: A:N.274 Salt bridges: A:K.309 SO4.6: 4 residues within 4Å: Chain A: Y.323, R.361, L.465, W.468 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.323 Water bridges: A:R.361, A:R.361, A:Q.394 Salt bridges: A:R.361 SO4.7: 7 residues within 4Å: Chain A: P.401, P.471, Y.472, H.474, S.482, V.483, G.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.471, A:S.482 Salt bridges: A:H.474 SO4.8: 4 residues within 4Å: Chain A: R.453, G.454, R.457, S.458 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.454, A:S.458 Water bridges: A:R.457, A:R.457 Salt bridges: A:R.453, A:R.457

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: F.253, G.258, S.259, S.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.260, A:S.260 GOL.10: 4 residues within 4Å: Chain A: G.111, H.211, Y.235 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.111, A:G.115 GOL.11: 3 residues within 4Å: Chain A: Y.126, R.222, Y.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.222, A:R.222 Water bridges: A:Y.126, A:Q.172, A:Y.411

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
A

5'-3' exonuclease PLD3

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