SMTL ID : 4q40.3 (3 other biounits)

Crystal structure of Schistosoma mansoni arginase in complex with L-valine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-trimer

Ligands

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: Q.372, I.374 Chain B: F.104, L.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.372 IMD.7: 6 residues within 4Å: Chain A: Q.102, G.105, K.107, A.187, S.188, G.189 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.102, A:K.107 IMD.8: 4 residues within 4Å: Chain B: Q.372, I.374 Chain C: F.104, L.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.372 IMD.14: 6 residues within 4Å: Chain B: Q.102, G.105, K.107, A.187, S.188, G.189 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.102, B:K.107 IMD.15: 4 residues within 4Å: Chain A: F.104, L.184 Chain C: Q.372, I.374 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.372 IMD.21: 6 residues within 4Å: Chain C: Q.102, G.105, K.107, A.187, S.188, G.189 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.102, C:K.107

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

MN.2: 5 residues within 4Å: Chain A: H.152, D.175, D.179, D.283 Ligands: MN.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.152, A:D.175, A:D.179, A:D.283, H2O.2, H2O.2 MN.3: 5 residues within 4Å: Chain A: D.175, H.177, D.283, D.285 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:H.177, A:D.283, A:D.285, H2O.2 MN.9: 5 residues within 4Å: Chain B: H.152, D.175, D.179, D.283 Ligands: MN.10 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.152, B:D.175, B:D.179, B:D.283, H2O.12, H2O.12 MN.10: 5 residues within 4Å: Chain B: D.175, H.177, D.283, D.285 Ligands: MN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.175, B:H.177, B:D.283, B:D.285, H2O.12 MN.16: 5 residues within 4Å: Chain C: H.152, D.175, D.179, D.283 Ligands: MN.17 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.152, C:D.175, C:D.179, C:D.283, H2O.21, H2O.21 MN.17: 5 residues within 4Å: Chain C: D.175, H.177, D.283, D.285 Ligands: MN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.175, C:H.177, C:D.283, C:D.285, H2O.21

3 x VAL: VALINE(Non-covalent)

VAL.4: 9 residues within 4Å: Chain A: H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, T.297 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:T.297 Hydrogen bonds: A:N.181, A:S.188, A:D.234 Water bridges: A:S.188, A:S.188, A:G.193, A:G.193, A:D.234 VAL.11: 9 residues within 4Å: Chain B: H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, T.297 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:T.297 Hydrogen bonds: B:N.181, B:S.188, B:D.234 Water bridges: B:S.188, B:S.188, B:G.193, B:G.193, B:D.234 VAL.18: 9 residues within 4Å: Chain C: H.177, D.179, N.181, S.188, H.192, G.193, D.234, E.237, T.297 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:T.297 Hydrogen bonds: C:N.181, C:S.188, C:D.234 Water bridges: C:S.188, C:S.188, C:G.193, C:G.193, C:D.234

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: N.53, I.59, Y.62, E.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.94 Water bridges: A:E.94 GOL.6: 5 residues within 4Å: Chain A: 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.12: 4 residues within 4Å: Chain B: N.53, I.59, Y.62, E.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.94 Water bridges: B:E.94 GOL.13: 5 residues within 4Å: Chain B: 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.19: 4 residues within 4Å: Chain C: N.53, I.59, Y.62, E.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.94 Water bridges: C:E.94 GOL.20: 5 residues within 4Å: Chain C: 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

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

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