SMTL ID : 4iu4.1

Crystal structure of Leishmania mexicana arginase in complex with inhibitor BEC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.115, D.138, D.142, D.244 Ligands: MN.2, S2C.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.115, A:D.138, A:D.142, A:D.244 MN.2: 6 residues within 4Å: Chain A: D.138, H.140, D.244, D.246 Ligands: MN.1, S2C.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:H.140, A:D.244, A:D.246, A:D.246 MN.6: 6 residues within 4Å: Chain B: H.115, D.138, D.142, D.244 Ligands: MN.7, S2C.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.115, B:D.138, B:D.142, B:D.244 MN.7: 6 residues within 4Å: Chain B: D.138, H.140, D.244, D.246 Ligands: MN.6, S2C.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.138, B:H.140, B:D.244, B:D.246, B:D.246 MN.11: 6 residues within 4Å: Chain C: H.115, D.138, D.142, D.244 Ligands: MN.12, S2C.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.115, C:D.138, C:D.142, C:D.244 MN.12: 6 residues within 4Å: Chain C: D.138, H.140, D.244, D.246 Ligands: MN.11, S2C.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.138, C:H.140, C:D.244, C:D.246, C:D.246

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.267, F.271, E.274, L.320 Chain B: M.212, H.213, D.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.213 Water bridges: B:G.262 GOL.8: 7 residues within 4Å: Chain B: R.267, F.271, E.274, L.320 Chain C: M.212, H.213, D.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.213 Water bridges: C:G.262 GOL.13: 7 residues within 4Å: Chain A: M.212, H.213, D.216 Chain C: R.267, F.271, E.274, L.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.213 Water bridges: A:G.262

3 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: G.219 Chain B: D.216, R.217, G.219 Ligands: BME.9, BME.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.220 BME.9: 6 residues within 4Å: Chain B: G.219 Chain C: D.216, R.217, G.219 Ligands: BME.4, BME.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:I.220 BME.14: 6 residues within 4Å: Chain A: D.216, R.217, G.219 Chain C: G.219 Ligands: BME.4, BME.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.220

3 x S2C: S-2-(BORONOETHYL)-L-CYSTEINE(Non-covalent)

S2C.5: 16 residues within 4Å: Chain A: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, D.195, E.198, D.244, D.246, T.258, E.289 Ligands: MN.1, MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:H.115, A:N.144, A:S.151, A:D.195, A:D.195, A:T.258, A:E.289 Water bridges: A:D.142, A:S.151, A:N.153, A:N.153, A:N.153, A:T.258, A:T.258 S2C.10: 16 residues within 4Å: Chain B: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, D.195, E.198, D.244, D.246, T.258, E.289 Ligands: MN.6, MN.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.115, B:N.144, B:S.151, B:D.195, B:D.195, B:T.258, B:E.289 Water bridges: B:D.142, B:S.151, B:N.153, B:N.153, B:N.153, B:T.258, B:T.258 S2C.15: 16 residues within 4Å: Chain C: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, D.195, E.198, D.244, D.246, T.258, E.289 Ligands: MN.11, MN.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:H.115, C:N.144, C:S.151, C:D.195, C:D.195, C:T.258, C:E.289 Water bridges: C:D.142, C:S.151, C:N.153, C:N.153, C:N.153, C:T.258, C:T.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Antonio, E.L. et al., Crystal structure of arginase from Leishmania mexicana and implications for the inhibition of polyamine biosynthesis in parasitic infections. Arch.Biochem.Biophys. (2013)

Release Date

2013-01-30

Peptides

Arginase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Arginase

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