SMTL ID : 4q3r.2 (3 other biounits)

Crystal structure of Schistosoma mansoni arginase in complex with inhibitor ABHDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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, XA2.9 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, XA2.9 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.12: 6 residues within 4Å: Chain B: H.152, D.175, D.179, D.283 Ligands: MN.13, XA2.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.152, B:D.175, B:D.179, B:D.283 MN.13: 6 residues within 4Å: Chain B: D.175, H.177, D.283, D.285 Ligands: MN.12, XA2.20 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.23: 6 residues within 4Å: Chain C: H.152, D.175, D.179, D.283 Ligands: MN.24, XA2.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.152, C:D.175, C:D.179, C:D.283 MN.24: 6 residues within 4Å: Chain C: D.175, H.177, D.283, D.285 Ligands: MN.23, XA2.31 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

12 x CS: CESIUM ION(Non-covalent)

CS.3: 3 residues within 4Å: Chain A: Y.248, D.253 Ligands: CL.7 No protein-ligand interaction detected (PLIP) CS.4: 2 residues within 4Å: Chain A: L.332, G.334 No protein-ligand interaction detected (PLIP) CS.5: 4 residues within 4Å: Chain A: R.69, K.70, S.71 Ligands: CL.8 No protein-ligand interaction detected (PLIP) CS.6: 2 residues within 4Å: Chain A: D.211, E.214 No protein-ligand interaction detected (PLIP) CS.14: 3 residues within 4Å: Chain B: Y.248, D.253 Ligands: CL.18 No protein-ligand interaction detected (PLIP) CS.15: 2 residues within 4Å: Chain B: L.332, G.334 No protein-ligand interaction detected (PLIP) CS.16: 4 residues within 4Å: Chain B: R.69, K.70, S.71 Ligands: CL.19 No protein-ligand interaction detected (PLIP) CS.17: 2 residues within 4Å: Chain B: D.211, E.214 No protein-ligand interaction detected (PLIP) CS.25: 3 residues within 4Å: Chain C: Y.248, D.253 Ligands: CL.29 No protein-ligand interaction detected (PLIP) CS.26: 2 residues within 4Å: Chain C: L.332, G.334 No protein-ligand interaction detected (PLIP) CS.27: 4 residues within 4Å: Chain C: R.69, K.70, S.71 Ligands: CL.30 No protein-ligand interaction detected (PLIP) CS.28: 2 residues within 4Å: Chain C: D.211, E.214 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: Y.248, F.249 Ligands: CS.3 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.70, S.71 Ligands: CS.5 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: Y.248, F.249 Ligands: CS.14 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.70, S.71 Ligands: CS.16 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: Y.248, F.249 Ligands: CS.25 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: K.70, S.71 Ligands: CS.27 Ligand excluded by PLIP

3 x XA2: (R)-2-amino-6-borono-2-(1-(3,4-dichlorobenzyl)piperidin-4-yl)hexanoic acid(Non-covalent)

XA2.9: 18 residues within 4Å: Chain A: H.152, D.175, H.177, D.179, N.181, A.187, S.188, H.192, G.193, D.232, D.234, D.283, D.285, T.297, E.328 Chain C: E.79 Ligands: MN.1, MN.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.181, A:S.188, A:D.234, A:E.328 Water bridges: A:N.190, A:N.190, A:D.232, A:D.234, A:E.237, A:T.297, A:T.297, A:T.297 Salt bridges: A:D.232, A:D.234 Hydrophobic interactions: C:E.79 XA2.20: 18 residues within 4Å: Chain A: E.79 Chain B: H.152, D.175, H.177, D.179, N.181, A.187, S.188, H.192, G.193, D.232, D.234, D.283, D.285, T.297, E.328 Ligands: MN.12, MN.13 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.152, B:N.181, B:S.188, B:D.234, B:D.283, B:D.283, B:D.283, B:T.297 Water bridges: B:N.190, B:N.190, B:D.232, B:D.234, B:D.234, B:E.237, B:D.285, B:T.297 Salt bridges: B:D.232, B:D.234 Hydrophobic interactions: A:E.79 XA2.31: 18 residues within 4Å: Chain B: E.79 Chain C: H.152, D.175, H.177, D.179, N.181, A.187, S.188, H.192, G.193, D.232, D.234, D.283, D.285, T.297, E.328 Ligands: MN.23, MN.24 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.177, C:N.181, C:S.188, C:D.234, C:D.283, C:D.283, C:D.283, C:T.297 Water bridges: C:N.190, C:N.190, C:D.232, C:D.234, C:E.237, C:D.285, C:T.297 Salt bridges: C:D.232, C:D.234 Hydrophobic interactions: B:E.79

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: E.97, D.100, P.101, Q.102, K.107, W.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.100, A:M.106, A:W.108 Water bridges: A:R.103 GOL.11: 3 residues within 4Å: Chain A: N.53, Y.62, E.94 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.54 GOL.21: 6 residues within 4Å: Chain B: E.97, D.100, P.101, Q.102, K.107, W.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.100, B:M.106, B:W.108 Water bridges: B:R.103 GOL.22: 3 residues within 4Å: Chain B: N.53, Y.62, E.94 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.54 GOL.32: 6 residues within 4Å: Chain C: E.97, D.100, P.101, Q.102, K.107, W.108 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.100, C:M.106, C:W.108 Water bridges: C:R.103 GOL.33: 3 residues within 4Å: Chain C: N.53, Y.62, E.94 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.54

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
B

B
B

C
B

Arginase

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