SMTL ID : 5zeh.1

Crystal structure of Entamoeba histolytica Arginase in complex with L- Ornithine at 2.35 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x ORN: L-ornithine(Non-covalent)

ORN.1: 10 residues within 4Å: Chain A: H.142, D.144, N.146, S.151, S.153, H.157, G.158, D.194, E.197 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.146, A:S.153, A:H.157 Water bridges: A:T.255 ORN.5: 10 residues within 4Å: Chain B: H.142, D.144, N.146, P.152, S.153, H.157, G.158, D.194, E.197, T.255 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.146, B:S.153, B:H.157, B:D.194 Water bridges: B:S.192, B:D.194

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

MN.2: 6 residues within 4Å: Chain A: H.114, D.140, D.144, D.241 Ligands: ORN.1, MN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.114, A:D.140, A:D.144, A:D.241, H2O.1 MN.3: 6 residues within 4Å: Chain A: D.140, A.141, H.142, D.241, D.243 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:H.142, A:D.241, A:D.243, H2O.1 MN.6: 5 residues within 4Å: Chain B: H.114, D.140, D.144, D.241 Ligands: MN.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.114, B:D.140, B:D.144, B:D.241, H2O.2 MN.7: 5 residues within 4Å: Chain B: D.140, H.142, D.241, D.243 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.140, B:H.142, B:D.241, B:D.243, B:D.243

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: N.131, R.133, D.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malik, A. et al., Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential antiamoebic molecules. Febs J. (2019)

Release Date

2019-06-26

Peptides

Arginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arginase

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