SMTL ID : 8v05.1

Crystal structure of mouse PLD3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: T.109, N.111, E.124, L.127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain B: T.109, N.111, E.124, L.127 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: 6 residues within 4Å: Chain A: E.61, Y.212, N.213 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN.3, EDO.4 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: E.61, Y.212, N.213 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN.12, EDO.13 No protein-ligand interaction detected (PLIP)

2 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.3: 15 residues within 4Å: Chain A: E.61, A.62, V.63, A.77, T.78, T.79, S.80, N.81, P.82, Q.86, N.261, G.432, L.433, Q.436 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.64, A:Q.436 Hydrogen bonds: A:A.77, A:S.80 NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 15 residues within 4Å: Chain B: E.61, A.62, V.63, A.77, T.78, T.79, S.80, N.81, P.82, Q.86, N.261, G.432, L.433, Q.436 Ligands: NAG-NAG.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.64, B:Q.436 Hydrogen bonds: B:A.77, B:S.80

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

EDO.4: 6 residues within 4Å: Chain A: G.90, L.91, G.94, H.188, Y.212 Ligands: NAG-NAG.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.94, A:G.94, A:N.213 EDO.5: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:Q.252, A:T.282, A:T.282, A:K.286 EDO.8: 7 residues within 4Å: Chain A: D.324, R.328, E.332 Chain B: R.317, F.318, W.319, P.320 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.318, A:R.328 EDO.13: 6 residues within 4Å: Chain B: G.90, L.91, G.94, H.188, Y.212 Ligands: NAG-NAG.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.94, B:G.94, B:N.213 EDO.14: 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:T.282, B:T.282, B:K.286 EDO.17: 7 residues within 4Å: Chain A: R.317, F.318, W.319, P.320 Chain B: D.324, R.328, E.332 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.318, B:R.328

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 5 residues within 4Å: Chain A: K.139, R.141, Q.163, R.165, W.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.163, A:W.229 Water bridges: A:R.165 Salt bridges: A:K.139, A:R.165 ACT.15: 5 residues within 4Å: Chain B: K.139, R.141, Q.163, R.165, W.229 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.163, B:W.229 Water bridges: B:R.165 Salt bridges: B:K.139, B:R.165

2 x CYS: CYSTEINE(Non-covalent)

CYS.7: 4 residues within 4Å: Chain A: C.259, G.262, T.263, P.264 No protein-ligand interaction detected (PLIP) CYS.16: 4 residues within 4Å: Chain B: C.259, G.262, T.263, P.264 No protein-ligand interaction detected (PLIP)

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.9: 12 residues within 4Å: Chain A: F.104, Y.105, H.178, K.180, N.195, M.304, N.305, W.344, H.393, K.395, N.409, Y.414 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:H.178, A:N.195, A:N.305, A:H.393, A:K.395, A:N.409, A:Y.414 Water bridges: A:H.393 Salt bridges: A:H.178, A:K.180, A:H.393, A:K.395 TLA.18: 12 residues within 4Å: Chain B: F.104, Y.105, H.178, K.180, N.195, M.304, N.305, W.344, H.393, K.395, N.409, Y.414 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.178, B:N.195, B:N.305, B:H.393, B:K.395, B:N.409, B:Y.414 Water bridges: B:H.393 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
A

B
A

5'-3' exonuclease PLD3

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