SMTL ID : 7qbp.1

Crystal structure of R2-like ligand-binding oxidase from Saccharopolyspora Erythraea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.1: 5 residues within 4Å: Chain A: E.86, E.119, H.122 Ligands: FE.2, PLM.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.86, A:E.119, A:H.122, H2O.1, H2O.2 MN3.5: 5 residues within 4Å: Chain B: E.86, E.119, H.122 Ligands: FE.6, PLM.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.86, B:E.119, B:H.122, H2O.7, H2O.9

2 x FE: FE (III) ION(Non-covalent)

FE.2: 8 residues within 4Å: Chain A: F.115, E.119, Y.180, E.185, E.220, H.223 Ligands: MN3.1, PLM.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.119, A:E.185, A:E.220, A:H.223, H2O.2 FE.6: 8 residues within 4Å: Chain B: F.115, E.119, Y.180, E.185, E.220, H.223 Ligands: MN3.5, PLM.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.119, B:E.185, B:E.220, B:H.223, H2O.9

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 30 residues within 4Å: Chain A: S.74, M.77, L.78, Q.81, F.82, G.85, E.86, V.89, E.119, Y.149, F.153, Y.180, V.184, E.185, L.188, A.189, T.191, G.192, A.195, I.199, E.220, Q.259, I.260, R.263, T.271, L.275, I.277, L.280 Ligands: MN3.1, FE.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.78, A:F.82, A:I.277, A:L.280 PLM.7: 30 residues within 4Å: Chain B: S.74, M.77, L.78, Q.81, F.82, G.85, E.86, V.89, E.119, Y.149, F.153, Y.180, V.184, E.185, L.188, A.189, T.191, G.192, A.195, I.199, E.220, Q.259, I.260, R.263, T.271, L.275, I.277, L.280 Ligands: MN3.5, FE.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.78, B:F.82, B:I.277, B:L.280

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

SO4.4: 5 residues within 4Å: Chain A: L.190, R.221, R.287, R.290, R.291 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.221, A:R.287, A:R.290, A:R.291 SO4.8: 5 residues within 4Å: Chain B: L.190, R.221, R.287, R.290, R.291 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:R.221, B:R.287, B:R.290, B:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diamanti, R. et al., Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase. Febs Lett. (2022)

Release Date

2022-04-06

Peptides

R2-like ligand binding oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

R2-like ligand binding oxidase