SMTL ID : 7kil.1

Crystal structure of the mouse lipin-1 M-Lip domain with zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: L.12, D.46, P.47, N.48 Ligands: CL.6, CL.7, CL.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.46, A:D.46 ZN.2: 2 residues within 4Å: Chain A: D.88 Chain B: A.42 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.88, H2O.3, H2O.4, H2O.4, H2O.4 ZN.3: 2 residues within 4Å: Chain A: K.79, E.83 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.83, A:E.83, H2O.2 ZN.4: 2 residues within 4Å: Chain A: D.18, R.20 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.18, A:D.18, H2O.4 ZN.5: 4 residues within 4Å: Chain A: H.19, P.91 Ligands: CL.10, CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.19 ZN.12: 4 residues within 4Å: Chain B: D.46, P.47, N.48 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.46, B:D.46 ZN.13: 5 residues within 4Å: Chain A: A.42 Chain B: D.88, K.89 Ligands: CL.16, CL.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, H2O.6 ZN.14: 4 residues within 4Å: Chain B: K.79, E.83 Ligands: CL.18, CL.19 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.83, B:E.83, H2O.8

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

CL.6: 6 residues within 4Å: Chain A: L.12, D.46, N.48 Ligands: ZN.1, CL.7, CL.8 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: D.46, P.47, N.48 Ligands: ZN.1, CL.6, CL.8 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: L.12, D.46 Ligands: ZN.1, CL.6, CL.7 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: C.13, G.14, G.15, R.20 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: H.19, P.91 Ligands: ZN.5, CL.11 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: H.19, P.91 Ligands: ZN.5, CL.10 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: L.12, D.46, N.48 Ligands: ZN.12 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: A.42 Chain B: D.88, K.89 Ligands: ZN.13, CL.17 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain A: P.41 Chain B: I.85, D.88, K.89 Ligands: ZN.13, CL.16 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: K.79, E.83 Ligands: ZN.14, CL.19 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: E.83 Ligands: ZN.14, CL.18 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, W. et al., The middle lipin domain adopts a membrane-binding dimeric protein fold. Nat Commun (2021)

Release Date

2021-07-07

Peptides

Isoform 2 of Phosphatidate phosphatase LPIN1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 2 of Phosphatidate phosphatase LPIN1

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