SMTL ID : 8v07.1 (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: 3 residues within 4Å: Chain A: E.61, Y.212, N.213 No protein-ligand interaction detected (PLIP)

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.2: 9 residues within 4Å: Chain A: E.61, A.62, V.63, N.81, P.82, N.261, G.432, L.433, Q.436 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NAG-NAG.3: 8 residues within 4Å: Chain B: E.61, A.62, V.63, S.80, N.261, G.432, L.433, Q.436 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.436

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 6 residues within 4Å: Chain A: K.139, R.141, Q.163, R.165, E.226, W.229 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.141 Water bridges: A:K.139, A:R.165, A:R.165 Salt bridges: A:K.139, A:R.141, A:R.165

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: H.346, P.387, Y.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.388 GOL.7: 7 residues within 4Å: Chain A: G.90, L.91, G.94, A.95, V.184, H.188, Y.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.94 Water bridges: A:L.91 GOL.10: 3 residues within 4Å: Chain B: H.346, P.387, Y.388 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.346, B:Y.388 Water bridges: B:H.346, B:A.389

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.6: 4 residues within 4Å: Chain A: N.305, E.311, N.409, Y.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.409, A:Y.414

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

PO4.8: 8 residues within 4Å: Chain A: F.104, H.178, K.180, N.195, M.304, H.393, K.395, N.409 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.195, A:N.409 Water bridges: A:Y.105 Salt bridges: A:H.178, A:K.180, A:H.393, A:K.395 PO4.11: 8 residues within 4Å: Chain B: F.104, H.178, K.180, N.195, M.304, H.393, K.395, N.409 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.195, B:N.409 Water bridges: B:H.393, B:K.395, B:Y.414 Salt bridges: B:H.178, B:K.180, B:H.393, B:K.395

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

NAG.9: 3 residues within 4Å: Chain B: E.61, Y.212, N.213 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.212 Hydrogen bonds: B:E.61 Water bridges: B:N.213

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
B

B
A

5'-3' exonuclease PLD3

Related Entries With Identical Sequence