- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x XYS: alpha-D-xylopyranose(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.54, D.81, D.83
- Ligands: PPR.6
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.81, H2O.1, H2O.1, H2O.1
MG.8: 4 residues within 4Å:- Chain B: D.54, D.81, D.83
- Ligands: PPR.12
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.81, H2O.12, H2O.12, H2O.12
MG.14: 4 residues within 4Å:- Chain C: D.54, D.81, D.83
- Ligands: PPR.18
4 PLIP interactions:1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:D.81, H2O.23, H2O.23, H2O.23
MG.20: 4 residues within 4Å:- Chain D: D.54, D.81, D.83
- Ligands: PPR.24
4 PLIP interactions:1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:D.81, H2O.35, H2O.35, H2O.35
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.3: 7 residues within 4Å:- Chain A: H.23, L.46, S.49
- Ligands: CL.4, CL.5, CL.22, CL.23
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.49
NA.9: 7 residues within 4Å:- Chain B: H.23, L.46, S.49
- Ligands: CL.10, CL.11, CL.16, CL.17
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.23, B:S.49
NA.15: 7 residues within 4Å:- Chain C: H.23, L.46, S.49
- Ligands: CL.10, CL.11, CL.16, CL.17
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:H.23, C:S.49
NA.21: 7 residues within 4Å:- Chain D: H.23, L.46, S.49
- Ligands: CL.4, CL.5, CL.22, CL.23
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:H.23, D:S.49
- 8 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 8 residues within 4Å:- Chain A: H.23, N.24
- Chain D: N.24
- Ligands: NA.3, CL.5, NA.21, CL.22, CL.23
Ligand excluded by PLIPCL.5: 7 residues within 4Å:- Chain A: M.66
- Chain D: M.66
- Ligands: NA.3, CL.4, NA.21, CL.22, CL.23
Ligand excluded by PLIPCL.10: 8 residues within 4Å:- Chain B: H.23, N.24
- Chain C: N.24
- Ligands: NA.9, CL.11, NA.15, CL.16, CL.17
Ligand excluded by PLIPCL.11: 7 residues within 4Å:- Chain B: M.66
- Chain C: M.66
- Ligands: NA.9, CL.10, NA.15, CL.16, CL.17
Ligand excluded by PLIPCL.16: 8 residues within 4Å:- Chain B: N.24
- Chain C: H.23, N.24
- Ligands: NA.9, CL.10, CL.11, NA.15, CL.17
Ligand excluded by PLIPCL.17: 7 residues within 4Å:- Chain B: M.66
- Chain C: M.66
- Ligands: NA.9, CL.10, CL.11, NA.15, CL.16
Ligand excluded by PLIPCL.22: 8 residues within 4Å:- Chain A: N.24
- Chain D: H.23, N.24
- Ligands: NA.3, CL.4, CL.5, NA.21, CL.23
Ligand excluded by PLIPCL.23: 7 residues within 4Å:- Chain A: M.66
- Chain D: M.66
- Ligands: NA.3, CL.4, CL.5, NA.21, CL.22
Ligand excluded by PLIP- 4 x PPR: PHOSPHONOPYRUVATE(Non-covalent)
PPR.6: 10 residues within 4Å:- Chain A: W.40, S.42, G.43, F.44, D.81, R.155, H.186, R.188, G.235
- Ligands: MG.2
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:G.43, A:F.44, A:D.54, A:R.155, A:R.155, A:H.186, A:R.188, A:R.188
- Water bridges: A:D.54, A:N.236, A:N.236, A:N.236
PPR.12: 10 residues within 4Å:- Chain B: W.40, S.42, G.43, F.44, D.81, R.155, H.186, R.188, G.235
- Ligands: MG.8
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:G.43, B:F.44, B:D.54, B:R.155, B:R.155, B:H.186, B:R.188, B:R.188
- Water bridges: B:D.54, B:N.236, B:N.236, B:N.236
PPR.18: 10 residues within 4Å:- Chain C: W.40, S.42, G.43, F.44, D.81, R.155, H.186, R.188, G.235
- Ligands: MG.14
14 PLIP interactions:14 interactions with chain C- Hydrogen bonds: C:G.43, C:F.44, C:D.54, C:R.155, C:R.155, C:H.186, C:R.188, C:R.188
- Water bridges: C:D.54, C:D.54, C:E.110, C:N.236, C:N.236, C:N.236
PPR.24: 10 residues within 4Å:- Chain D: W.40, S.42, G.43, F.44, D.81, R.155, H.186, R.188, G.235
- Ligands: MG.20
14 PLIP interactions:14 interactions with chain D- Hydrogen bonds: D:G.43, D:F.44, D:D.54, D:R.155, D:R.155, D:H.186, D:R.188, D:R.188
- Water bridges: D:D.54, D:D.54, D:E.110, D:N.236, D:N.236, D:N.236
- 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
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x XYS: alpha-D-xylopyranose(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 8 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x PPR: PHOSPHONOPYRUVATE(Non-covalent)
- 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
AB
AC
AD
A