SMTL ID : 6ae9.1

X-ray structure of the photosystem II phosphatase PBCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.37, G.38, S.40 Ligands: PO4.4, MN.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.37, A:G.38, H2O.1, H2O.2 MG.2: 6 residues within 4Å: Chain A: D.110, D.133, D.168, K.239 Ligands: PO4.4, MN.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.168, H2O.2, H2O.2, H2O.4, H2O.5 MG.3: 3 residues within 4Å: Chain A: D.110, E.129, D.172 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: D.37, G.38 Ligands: PO4.10, MN.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.37, B:G.38, H2O.13, H2O.14 MG.8: 4 residues within 4Å: Chain B: D.110, D.168 Ligands: PO4.10, MN.13 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.168, H2O.13, H2O.14, H2O.14, H2O.17 MG.9: 3 residues within 4Å: Chain B: D.110, E.129, D.172 No protein-ligand interaction detected (PLIP)

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

PO4.4: 9 residues within 4Å: Chain A: D.37, G.38, V.39, S.40, D.168, N.241 Ligands: MG.1, MG.2, MN.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.40, A:N.241 Water bridges: A:S.40, A:D.133, A:K.239, A:N.241 Salt bridges: A:K.239 PO4.10: 9 residues within 4Å: Chain B: D.37, G.38, V.39, S.40, D.168, N.241 Ligands: MG.7, MG.8, MN.13 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.37, B:S.40, B:N.241, B:N.241 Water bridges: B:K.14, B:S.40, B:D.242, B:D.242 Salt bridges: B:K.239

3 x POG: (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL(Non-covalent)

POG.5: 9 residues within 4Å: Chain A: W.42, K.45, H.130, Y.131, C.134, Q.137, E.141, I.143, Q.145 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.42, A:H.130, A:Y.131, A:Q.137 Hydrogen bonds: A:K.45 POG.11: 8 residues within 4Å: Chain B: G.41, W.42, K.45, V.87, H.130, C.134, Q.137, E.141 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.87, B:Q.137 Hydrogen bonds: B:K.45 POG.12: 7 residues within 4Å: Chain A: S.219 Chain B: F.175, E.178, F.209, M.215, E.216, S.219 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.175, B:F.209, B:E.216

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

MN.6: 7 residues within 4Å: Chain A: D.37, D.168, G.169, N.241 Ligands: MG.1, MG.2, PO4.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:D.168, H2O.1 MN.13: 7 residues within 4Å: Chain B: D.37, D.168, G.169, N.241 Ligands: MG.7, MG.8, PO4.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.37, B:D.168, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Structural Insights into Substrate Selectivity, Catalytic Mechanism, and Redox Regulation of Rice Photosystem II Core Phosphatase. Mol Plant (2019)

Release Date

2019-01-02

Peptides

Probable protein phosphatase 2C 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable protein phosphatase 2C 1