SMTL ID : 8q1k.1

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: E.11, A.12, V.13, P.32, Q.36, Y.164, N.213, G.383, G.384, L.385, Q.388 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.164

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: 5 residues within 4Å: Chain A: E.11, Y.164, N.165 Ligands: NAG-NAG-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: Y.164, N.165 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

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.4: 11 residues within 4Å: Chain B: E.11, A.12, V.13, G.30, P.32, Q.36, N.213, G.384, L.385, Q.388 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP)

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: P.5, C.6, Y.7, E.209, I.210, P.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.6 Water bridges: A:I.210 EDO.6: 3 residues within 4Å: Chain A: G.297, A.415, R.417 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: R.382, G.383, R.386, S.387 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.383, A:R.386 EDO.14: 6 residues within 4Å: Chain B: N.203, E.205, G.232, T.234, P.235, K.238 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.205, B:K.238 Water bridges: B:K.238 EDO.15: 2 residues within 4Å: Chain B: N.60, E.74 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.60 Water bridges: B:N.60, B:E.67, B:Q.71, B:E.74 EDO.16: 2 residues within 4Å: Chain B: R.196, R.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.196, B:R.201, B:R.201 EDO.17: 3 residues within 4Å: Chain A: P.267 Chain B: R.248, R.285 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.269

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

PO4.8: 3 residues within 4Å: Chain A: D.8, S.167, R.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.8 Water bridges: A:D.8, A:D.8 Salt bridges: A:R.171 PO4.9: 2 residues within 4Å: Chain A: A.186, G.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.187 Water bridges: A:K.123, A:S.188, A:S.188 Salt bridges: A:K.123 PO4.10: 5 residues within 4Å: Chain A: K.288, R.290, R.314, D.321, Q.323 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.323 Water bridges: A:K.288, A:K.288, A:R.290, A:R.290, A:R.314 Salt bridges: A:K.288, A:R.290, A:R.314 PO4.11: 6 residues within 4Å: Chain A: F.54, Y.55, H.130, K.132, N.147, H.345 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.147, A:N.147 Water bridges: A:H.345, A:K.347, A:K.347, A:K.347, A:N.361 Salt bridges: A:H.130, A:K.132, A:H.345, A:K.347 PO4.18: 6 residues within 4Å: Chain B: F.54, Y.55, H.130, K.132, N.147, H.345 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.147, B:N.147 Water bridges: B:Y.55, B:H.345, B:H.345, B:H.345, B:K.347, B:N.361, B:N.361 Salt bridges: B:H.130, B:K.132, B:H.345, B:K.347 PO4.19: 5 residues within 4Å: Chain B: K.288, R.290, R.314, D.321, Q.323 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.323 Water bridges: B:R.290, B:R.290, B:R.290, B:Q.323 Salt bridges: B:R.290, B:R.314 PO4.20: 3 residues within 4Å: Chain B: K.123, A.186, G.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.187 Water bridges: B:K.123, B:S.188, B:S.188 Salt bridges: B:K.123 PO4.21: 4 residues within 4Å: Chain B: R.91, Q.115, R.117, W.181 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.115, B:W.181 Water bridges: B:N.89, B:N.89, B:R.91, B:R.117, B:R.117, B:R.117 Salt bridges: B:R.91, B:R.117

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.12: 5 residues within 4Å: Chain A: A.224, P.235, D.236, L.237, F.367 No protein-ligand interaction detected (PLIP) MN.13: 2 residues within 4Å: Chain A: N.246, A.354 No protein-ligand interaction detected (PLIP) MN.22: 5 residues within 4Å: Chain B: A.224, P.235, D.236, L.237, F.367 No protein-ligand interaction detected (PLIP) MN.23: 2 residues within 4Å: Chain B: N.246, A.354 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roske, Y. et al., Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res. (2024)

Release Date

2023-12-06

Peptides

5'-3' exonuclease PLD3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-3' exonuclease PLD3