SMTL ID : 2dua.1

Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.1: 2 residues within 4Å: Chain A: E.32, S.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.75, A:S.75 Water bridges: A:E.32, A:T.73, A:T.73 XYS.7: 2 residues within 4Å: Chain B: E.32, S.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.75, B:S.75 Water bridges: B:E.32, B:T.73, B:T.73 XYS.13: 2 residues within 4Å: Chain C: E.32, S.75 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.75, C:S.75 Water bridges: C:E.32, C:T.73, C:T.73 XYS.19: 2 residues within 4Å: Chain D: E.32, S.75 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.75, D:S.75 Water bridges: D:E.32, D:T.73, D:T.73

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 8 residues within 4Å: Chain A: W.40, S.42, G.43, F.44, D.81, R.155, G.235 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.40, A:G.43, A:F.44 Water bridges: A:R.155, A:R.155 Salt bridges: A:R.155 OXL.8: 8 residues within 4Å: Chain B: W.40, S.42, G.43, F.44, D.81, R.155, G.235 Ligands: MG.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.40, B:G.43, B:F.44 Water bridges: B:R.155, B:R.155 Salt bridges: B:R.155 OXL.14: 8 residues within 4Å: Chain C: W.40, S.42, G.43, F.44, D.81, R.155, G.235 Ligands: MG.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.40, C:G.43, C:F.44 Water bridges: C:E.110, C:R.155 Salt bridges: C:R.155 OXL.20: 8 residues within 4Å: Chain D: W.40, S.42, G.43, F.44, D.81, R.155, G.235 Ligands: MG.21 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:W.40, D:G.43, D:F.44 Water bridges: D:E.110, D:R.155 Salt bridges: D:R.155

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: G.43, F.44, D.54, D.81, D.83 Ligands: OXL.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.81, H2O.1, H2O.1, H2O.1 MG.9: 6 residues within 4Å: Chain B: G.43, F.44, D.54, D.81, D.83 Ligands: OXL.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.81, H2O.14, H2O.14, H2O.14 MG.15: 6 residues within 4Å: Chain C: G.43, F.44, D.54, D.81, D.83 Ligands: OXL.14 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.81, H2O.27, H2O.27, H2O.27 MG.21: 6 residues within 4Å: Chain D: G.43, F.44, D.54, D.81, D.83 Ligands: OXL.20 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.81, H2O.40, H2O.40, H2O.40

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: H.23, L.46, S.49 Ligands: CL.5, CL.6, CL.23, CL.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.23, A:S.49 NA.10: 7 residues within 4Å: Chain B: H.23, L.46, S.49 Ligands: CL.11, CL.12, CL.17, CL.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.49, B:S.49 NA.16: 7 residues within 4Å: Chain C: H.23, L.46, S.49 Ligands: CL.11, CL.12, CL.17, CL.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.23, C:S.49 NA.22: 7 residues within 4Å: Chain D: H.23, L.46, S.49 Ligands: CL.5, CL.6, CL.23, CL.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.49

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

CL.5: 7 residues within 4Å: Chain A: M.66 Chain D: M.66 Ligands: NA.4, CL.6, NA.22, CL.23, CL.24 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: N.24 Chain D: N.24 Ligands: NA.4, CL.5, NA.22, CL.23, CL.24 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: M.66 Chain C: M.66 Ligands: NA.10, CL.12, NA.16, CL.17, CL.18 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain B: N.24 Chain C: N.24 Ligands: NA.10, CL.11, NA.16, CL.17, CL.18 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain B: M.66 Chain C: M.66 Ligands: NA.10, CL.11, CL.12, NA.16, CL.18 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain B: N.24 Chain C: N.24 Ligands: NA.10, CL.11, CL.12, NA.16, CL.17 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain A: M.66 Chain D: M.66 Ligands: NA.4, CL.5, CL.6, NA.22, CL.24 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain A: N.24 Chain D: N.24 Ligands: NA.4, CL.5, CL.6, NA.22, CL.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C.C.H. et al., Structure and Kinetics of Phosphonopyruvate Hydrolase from Voriovorax sp. Pal2: New Insight into the Divergence of Catalysis within the PEP Mutase/Isocitrate Lyase Superfamily. Biochemistry (2006)

Release Date

2006-10-03

Peptides

Phosphonopyruvate hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Phosphonopyruvate hydrolase

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