SMTL ID : 8brp.2 (1 other biounit)

Peptide Arginase OspR from the cyanobacterium Kamptonema sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.40, E.41, H.42, D.166, D.168 Ligands: MN.2, ACT.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.40, A:H.42, A:D.168, A:D.168, ACT.3 MN.2: 6 residues within 4Å: Chain A: H.13, D.40, D.44, D.166 Ligands: MN.1, ACT.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.13, A:D.40, A:D.44, A:D.166, ACT.3 MN.4: 6 residues within 4Å: Chain B: D.40, H.42, D.166, D.168 Ligands: MN.5, ACT.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.40, B:H.42, B:D.166, B:D.168 MN.5: 6 residues within 4Å: Chain B: H.13, D.40, D.44, D.166 Ligands: MN.4, ACT.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.13, B:D.40, B:D.44, B:D.166, ACT.6

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

ACT.3: 9 residues within 4Å: Chain A: H.13, D.40, H.42, D.44, I.74, D.166, D.168 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.74 Water bridges: A:H.13 Salt bridges: A:H.13, A:H.42 ACT.6: 9 residues within 4Å: Chain B: H.13, D.40, H.42, D.44, I.74, D.166, D.168 Ligands: MN.4, MN.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.74 Salt bridges: B:H.13, B:H.42

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: S.70, E.71, L.72, T.73 Chain B: R.201, W.204, G.205, N.207, A.208 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.72, B:A.208, B:A.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mordhorst, S. et al., Structural and Biochemical Insights into Post-Translational Arginine-to-Ornithine Peptide Modifications by an Atypical Arginase. Acs Chem.Biol. (2023)

Release Date

2023-03-01

Peptides

Peptide arginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Peptide arginase

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