SMTL ID : 8v07.2 (1 other biounit)

Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 30 days

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 4 residues within 4Å: Chain A: E.61, Y.212, N.213 Ligands: NAG-NAG-BMA-MAN.2 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 11 residues within 4Å: Chain A: E.61, A.62, V.63, N.81, P.82, Q.86, N.261, G.432, L.433, Q.436 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81

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.3: 8 residues within 4Å: Chain B: E.61, A.62, V.63, P.82, N.261, G.432, L.433, Q.436 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: Y.212, N.213 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: H.346, P.387, Y.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.346, A:Y.388 GOL.7: 5 residues within 4Å: Chain B: G.90, L.91, G.94, H.188, Y.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.91 Water bridges: B:L.91, B:Y.212 GOL.8: 9 residues within 4Å: Chain B: N.251, Q.252, E.253, S.279, G.280, R.281, T.282, P.283, K.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.252, B:E.253, B:S.279, B:K.286

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

PO4.6: 8 residues within 4Å: Chain A: F.104, H.178, K.180, N.195, M.304, H.393, K.395, N.409 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.195, A:N.409 Salt bridges: A:H.178, A:K.180, A:H.393, A:K.395 PO4.9: 7 residues within 4Å: Chain B: F.104, H.178, K.180, N.195, M.304, H.393, N.409 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.195, B:N.409 Water bridges: B:Y.105, B:K.395 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
C

B
D

5'-3' exonuclease PLD3

Related Entries With Identical Sequence