SMTL ID : 5zef.1

Crystal structure of Entamoeba histolytica Arginase in complex with L- Norvaline at 2.01 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x NVA: NORVALINE(Non-covalent)

NVA.1: 8 residues within 4Å: Chain A: H.142, N.146, S.151, P.152, S.153, H.157, G.158, D.194 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.146, A:S.153, A:D.194 Water bridges: A:S.153, A:N.155, A:G.158, A:G.158, A:S.192, A:D.194, A:D.194, A:E.197, A:E.197 NVA.7: 8 residues within 4Å: Chain B: H.142, N.146, P.152, S.153, H.157, G.158, D.194, T.255 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.146, B:S.153, B:D.194 Water bridges: B:D.194, B:D.194

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

MN.2: 5 residues within 4Å: Chain A: H.114, D.140, D.144, D.241 Ligands: 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, H.142, D.241, D.243, T.255 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.8: 5 residues within 4Å: Chain B: H.114, D.140, D.144, D.241 Ligands: MN.9 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.7 MN.9: 5 residues within 4Å: Chain B: D.140, H.142, D.241, D.243 Ligands: MN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.140, B:H.142, B:D.241, B:D.243, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: T.173, S.174, M.176, P.177, H.178, Y.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.173, A:Y.179 GOL.5: 6 residues within 4Å: Chain A: I.66, T.67, P.69, S.88, V.89, E.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88, A:E.92

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

EDO.6: 3 residues within 4Å: Chain A: V.125, K.126, M.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.128 EDO.10: 2 residues within 4Å: Chain B: R.94, S.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.94, B:R.94, B:S.174

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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