SMTL ID : 8q1x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN- MAN- MAN- MAN: 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.1: 12 residues within 4Å: Chain A: E.22, A.23, V.24, G.41, P.43, Q.47, N.224, G.394, G.395, L.396, Q.399 Ligands: NAG-NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.40, A:T.40, A:G.41 NAG-NAG-MAN-MAN-MAN-MAN.3: 11 residues within 4Å: Chain B: E.22, A.23, V.24, G.41, P.43, Q.47, N.224, G.395, L.396, Q.399 Ligands: NAG-NAG.4 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: 5 residues within 4Å: Chain A: E.22, Y.175, N.176 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: Y.175, N.176 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP)

4 x PST: THYMIDINE-5'-THIOPHOSPHATE(Non-covalent)

PST.5: 10 residues within 4Å: Chain A: Y.66, N.158, D.160, M.267, W.307, Y.351, V.354, H.356 Ligands: PST.6, EDO.16 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.66, A:Y.351 Hydrogen bonds: A:D.160 Water bridges: A:Y.66, A:Y.66, A:N.158, A:R.162, A:R.162, A:R.162, A:Y.351 pi-Stacking: A:Y.351 PST.6: 9 residues within 4Å: Chain A: F.65, H.141, K.143, N.158, M.267, H.356, K.358, N.372 Ligands: PST.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.356, A:K.358, A:N.372 PST.22: 8 residues within 4Å: Chain B: Y.66, N.158, R.162, V.167, W.307, Y.351, H.356 Ligands: PST.23 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.66, B:Y.351 Water bridges: B:Y.66, B:Y.66, B:R.162, B:R.162, B:R.162 pi-Stacking: B:Y.351 PST.23: 7 residues within 4Å: Chain B: F.65, H.141, K.143, N.158, K.358, N.372 Ligands: PST.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.356, B:K.358, B:K.358, B:N.372 Water bridges: B:Y.377

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

PO4.7: 5 residues within 4Å: Chain A: K.299, R.301, R.325, D.332, Q.334 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.325, A:Q.334 Water bridges: A:R.301, A:R.301, A:R.301, A:R.301, A:R.301, A:R.301 Salt bridges: A:K.299, A:R.301 PO4.8: 3 residues within 4Å: Chain A: K.134, A.197, G.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.198 Salt bridges: A:K.134 PO4.24: 5 residues within 4Å: Chain B: K.299, R.301, R.325, D.332, Q.334 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.332, B:Q.334 Water bridges: B:R.301, B:R.301, B:R.301, B:R.325, B:R.325 Salt bridges: B:K.299, B:R.301, B:R.325

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

EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.10: 1 residues within 4Å: Chain A: N.72 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.70, A:E.85 EDO.11: 7 residues within 4Å: Chain A: N.214, E.216, G.243, R.244, T.245, P.246, K.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.245, A:K.249 EDO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: D.34, F.35, P.36, P.411 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.34, A:Y.412 EDO.14: 6 residues within 4Å: Chain A: P.16, C.17, Y.18, E.220, I.221, P.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.17 Water bridges: A:I.221 EDO.15: 4 residues within 4Å: Chain A: R.393, G.394, R.397, S.398 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.394, A:R.397 Water bridges: A:G.392, A:G.392, A:R.397, A:S.398 EDO.16: 2 residues within 4Å: Chain A: F.65 Ligands: PST.5 No protein-ligand interaction detected (PLIP) EDO.21: 7 residues within 4Å: Chain B: N.214, E.216, G.243, R.244, T.245, P.246, K.249 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.216, B:K.249 EDO.25: 6 residues within 4Å: Chain B: D.19, P.20, T.150, N.176, C.177, S.178 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.19, B:N.176, B:S.178 Water bridges: B:D.19, B:S.178 EDO.26: 5 residues within 4Å: Chain B: V.139, F.275, N.376, Y.377, T.381 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.376, B:T.381, B:T.381 Water bridges: B:E.274, B:S.374 EDO.27: 2 residues within 4Å: Chain B: P.237, P.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.237 EDO.28: 4 residues within 4Å: Chain B: R.393, G.394, R.397, S.398 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.394, B:R.397 Water bridges: B:G.392 EDO.29: 3 residues within 4Å: Chain B: N.71, Q.82, E.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.71, B:Q.82, B:E.85 Water bridges: B:N.71 EDO.30: 2 residues within 4Å: Chain B: R.207, R.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.212, B:R.212

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

MN.17: 2 residues within 4Å: Chain A: N.257, A.365 No protein-ligand interaction detected (PLIP) MN.31: 2 residues within 4Å: Chain B: N.257, A.365 No protein-ligand interaction detected (PLIP)

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

SO4.18: 4 residues within 4Å: Chain A: R.102, Q.126, R.128, W.192 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.126, A:W.192 Water bridges: A:R.102, A:R.102, A:R.128, A:R.128, A:R.128 Salt bridges: A:R.102, A:R.128 SO4.19: 4 residues within 4Å: Chain A: D.19, S.178, C.179, R.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.19 Water bridges: A:D.19, A:S.178 Salt bridges: A:R.182 SO4.32: 3 residues within 4Å: Chain B: K.134, A.197, G.198 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.198 Water bridges: B:K.134, B:K.134, B:K.134, B:S.199 Salt bridges: B:K.134 SO4.33: 5 residues within 4Å: Chain B: N.100, R.102, Q.126, R.128, W.192 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.100, B:Q.126, B:W.192 Water bridges: B:R.102, B:R.102, B:R.128, B:R.128 Salt bridges: B:R.102

2 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 5 residues within 4Å: Chain A: A.235, P.246, D.247, L.248, F.378 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.378, H2O.3 MG.34: 5 residues within 4Å: Chain B: A.235, P.246, D.247, L.248, F.378 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.378, H2O.26

Links

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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