SMTL ID : 6mtw.1

Lysosomal Phospholipase A2 in complex with Zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.67, S.70, Q.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.67, A:Q.74 Water bridges: A:N.67 NAG.2: 5 residues within 4Å: Chain A: L.355, P.356, S.358, N.366, T.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.355, A:T.368 Water bridges: A:S.358, A:S.358 NAG.8: 3 residues within 4Å: Chain B: N.67, S.70, Q.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.67, B:N.67, B:Q.74 Water bridges: B:S.70 NAG.9: 6 residues within 4Å: Chain B: L.355, P.356, S.358, E.362, N.366, T.368 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.355 Water bridges: B:S.358, B:S.358, B:E.359, B:E.362

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: Q.295, H.348, Q.349 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: Q.295, H.348, Q.349 Ligand excluded by PLIP

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.14, S.166, M.167, H.360 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.166, A:H.360, H2O.4, H2O.6 ZN.5: 3 residues within 4Å: Chain A: C.323 Ligands: ZN.6, ZN.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.323, H2O.1, H2O.7, H2O.7, H2O.7 ZN.6: 6 residues within 4Å: Chain A: K.248, D.308, S.309, C.323 Ligands: ZN.5, ZN.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.308, A:D.308, A:C.323, H2O.1 ZN.7: 3 residues within 4Å: Chain A: S.309 Ligands: ZN.5, ZN.6 No protein-ligand interaction detected (PLIP) ZN.11: 4 residues within 4Å: Chain B: D.14, S.166, M.167, H.360 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.166, B:H.360, H2O.11, H2O.13 ZN.12: 3 residues within 4Å: Chain B: C.323 Ligands: ZN.13, ZN.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.323, H2O.12, H2O.13, H2O.14 ZN.13: 6 residues within 4Å: Chain B: K.248, D.308, S.309, C.323 Ligands: ZN.12, ZN.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.308, B:D.308, B:C.323, H2O.7 ZN.14: 3 residues within 4Å: Chain B: S.309 Ligands: ZN.12, ZN.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bouley, R.A. et al., Structural Basis of Lysosomal Phospholipase A2Inhibition by Zn2. Biochemistry (2019)

Release Date

2019-03-20

Peptides

Group XV phospholipase A2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Group XV phospholipase A2

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