SMTL ID : 5hja.1

Crystal structure of Leishmania mexicana arginase in complex with inhibitor ABHDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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, XA2.3 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, XA2.3 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.5: 6 residues within 4Å: Chain B: H.115, D.138, D.142, D.244 Ligands: MN.6, XA2.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.115, B:D.138, B:D.142, B:D.244 MN.6: 6 residues within 4Å: Chain B: D.138, H.140, D.244, D.246 Ligands: MN.5, XA2.7 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.9: 6 residues within 4Å: Chain C: H.115, D.138, D.142, D.244 Ligands: MN.10, XA2.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.115, C:D.138, C:D.142, C:D.244 MN.10: 6 residues within 4Å: Chain C: D.138, H.140, D.244, D.246 Ligands: MN.9, XA2.11 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 XA2: (R)-2-amino-6-borono-2-(1-(3,4-dichlorobenzyl)piperidin-4-yl)hexanoic acid(Non-covalent)

XA2.3: 18 residues within 4Å: Chain A: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, R.192, A.193, V.194, D.195, D.244, D.246, T.258, E.289 Ligands: MN.1, MN.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.140 Hydrogen bonds: A:N.144, A:S.151, A:D.195, A:E.289 Water bridges: A:D.142, A:S.151, A:N.153, A:N.153, A:N.153, A:A.193, A:E.198, A:E.198, A:D.244, A:T.258 Salt bridges: A:D.195 XA2.7: 18 residues within 4Å: Chain B: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, R.192, A.193, V.194, D.195, D.244, D.246, T.258, E.289 Ligands: MN.5, MN.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.140 Hydrogen bonds: B:N.144, B:S.151, B:D.195, B:E.289 Water bridges: B:D.142, B:S.151, B:N.153, B:N.153, B:N.153, B:A.193, B:E.198, B:E.198, B:D.244, B:T.258 Salt bridges: B:D.195 XA2.11: 18 residues within 4Å: Chain C: H.115, D.138, H.140, D.142, N.144, S.151, H.155, G.156, R.192, A.193, V.194, D.195, D.244, D.246, T.258, E.289 Ligands: MN.9, MN.10 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:H.140 Hydrogen bonds: C:N.144, C:S.151, C:D.195, C:E.289 Water bridges: C:D.142, C:S.151, C:N.153, C:N.153, C:N.153, C:A.193, C:E.198, C:E.198, C:D.244, C:T.258 Salt bridges: C:D.195

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.267, L.270, 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:M.212, B:D.216 GOL.8: 8 residues within 4Å: Chain B: R.267, L.270, 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:M.212, C:D.216 GOL.12: 8 residues within 4Å: Chain A: M.212, H.213, D.216 Chain C: R.267, L.270, F.271, E.274, L.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.212, A:D.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Crystal structures of Leishmania mexicana arginase complexed with alpha , alpha-disubstituted boronic amino-acid inhibitors. Acta Crystallogr F Struct Biol Commun (2016)

Release Date

2016-04-13

Peptides

Arginase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Arginase

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