SMTL ID : 4q3u.3 (3 other biounits)

Crystal structure of Schistosoma mansoni arginase in complex with inhibitor nor-NOHA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.152, D.175, D.179, D.283 Ligands: MN.2, NNH.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.152, A:D.175, A:D.179, A:D.283 MN.2: 6 residues within 4Å: Chain A: D.175, H.177, D.283, D.285 Ligands: MN.1, NNH.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:H.177, A:D.283, A:D.285, A:D.285 MN.6: 6 residues within 4Å: Chain B: H.152, D.175, D.179, D.283 Ligands: MN.7, NNH.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.152, B:D.175, B:D.179, B:D.283 MN.7: 6 residues within 4Å: Chain B: D.175, H.177, D.283, D.285 Ligands: MN.6, NNH.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.175, B:H.177, B:D.283, B:D.285, B:D.285 MN.11: 6 residues within 4Å: Chain C: H.152, D.175, D.179, D.283 Ligands: MN.12, NNH.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.152, C:D.175, C:D.179, C:D.283 MN.12: 6 residues within 4Å: Chain C: D.175, H.177, D.283, D.285 Ligands: MN.11, NNH.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.175, C:H.177, C:D.283, C:D.285, C:D.285

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.97, D.100, P.101, Q.102, K.107, W.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.100, A:M.106, A:W.108 Water bridges: A:Q.102, A:R.103 GOL.4: 4 residues within 4Å: Chain A: N.53, I.59, Y.62, E.94 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain B: E.97, D.100, P.101, Q.102, K.107, W.108 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.100, B:M.106, B:W.108 Water bridges: B:Q.102, B:R.103 GOL.9: 4 residues within 4Å: Chain B: N.53, I.59, Y.62, E.94 No protein-ligand interaction detected (PLIP) GOL.13: 6 residues within 4Å: Chain C: E.97, D.100, P.101, Q.102, K.107, W.108 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.100, C:M.106, C:W.108 Water bridges: C:Q.102, C:R.103 GOL.14: 4 residues within 4Å: Chain C: N.53, I.59, Y.62, E.94 No protein-ligand interaction detected (PLIP)

3 x NNH: NOR-N-OMEGA-HYDROXY-L-ARGININE(Non-covalent)

NNH.5: 15 residues within 4Å: Chain A: H.152, D.175, H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, D.283, D.285, T.297 Ligands: MN.1, MN.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.181, A:S.188, A:D.234, A:T.297, A:T.297 Water bridges: A:S.188, A:G.193, A:T.297, A:T.297 Salt bridges: A:D.175, A:D.179, A:D.283, A:D.285, A:E.328 pi-Cation interactions: A:H.177, A:H.192 NNH.10: 15 residues within 4Å: Chain B: H.152, D.175, H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, D.283, D.285, T.297 Ligands: MN.6, MN.7 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.181, B:S.188, B:D.234, B:T.297, B:T.297, B:T.297 Water bridges: B:S.188, B:G.193, B:T.297, B:T.297 Salt bridges: B:D.175, B:D.179, B:D.283, B:D.285, B:E.328 pi-Cation interactions: B:H.177, B:H.192 NNH.15: 15 residues within 4Å: Chain C: H.152, D.175, H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, D.283, D.285, T.297 Ligands: MN.11, MN.12 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.181, C:S.188, C:D.234, C:T.297, C:T.297 Water bridges: C:S.188, C:G.193, C:T.297, C:T.297 Salt bridges: C:D.175, C:D.179, C:D.283, C:D.285, C:E.328 pi-Cation interactions: C:H.177, C:H.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Crystal Structure of Schistosoma mansoni Arginase, a Potential Drug Target for the Treatment of Schistosomiasis. Biochemistry (2014)

Release Date

2014-07-16

Peptides

Arginase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

Arginase

Related Entries With Identical Sequence