- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.66 Å
- Oligo State
- homo-octamer
- Ligands
- 16 x LAF: 5-FLUOROLEVULINIC ACID(Covalent)(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 3 residues within 4Å:- Chain A: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain A, 5 Ligand-Water interactions- Metal complexes: A:E.245, H2O.10, H2O.10, H2O.12, H2O.12, H2O.12
MG.10: 3 residues within 4Å:- Chain B: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain B, 5 Ligand-Water interactions- Metal complexes: B:E.245, H2O.23, H2O.24, H2O.24, H2O.24, H2O.24
MG.15: 3 residues within 4Å:- Chain C: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain C, 5 Ligand-Water interactions- Metal complexes: C:E.245, H2O.36, H2O.36, H2O.38, H2O.38, H2O.38
MG.22: 3 residues within 4Å:- Chain D: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain D, 5 Ligand-Water interactions- Metal complexes: D:E.245, H2O.48, H2O.50, H2O.50, H2O.50, H2O.50
MG.27: 3 residues within 4Å:- Chain E: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain E, 5 Ligand-Water interactions- Metal complexes: E:E.245, H2O.61, H2O.61, H2O.63, H2O.64, H2O.64
MG.34: 3 residues within 4Å:- Chain F: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain F, 5 Ligand-Water interactions- Metal complexes: F:E.245, H2O.74, H2O.76, H2O.76, H2O.76, H2O.76
MG.39: 3 residues within 4Å:- Chain G: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain G, 5 Ligand-Water interactions- Metal complexes: G:E.245, H2O.87, H2O.87, H2O.89, H2O.89, H2O.89
MG.46: 3 residues within 4Å:- Chain H: R.181, E.245, D.249
6 PLIP interactions:1 interactions with chain H, 5 Ligand-Water interactions- Metal complexes: H:E.245, H2O.100, H2O.101, H2O.101, H2O.102, H2O.102
- 8 x NA: SODIUM ION(Non-functional Binders)
NA.4: 6 residues within 4Å:- Chain A: D.127, A.129, D.131, S.175
- Ligands: LAF.1, LAF.2
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.127, A:S.175
NA.11: 4 residues within 4Å:- Chain B: D.127, S.175
- Ligands: LAF.6, LAF.7
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.127, B:S.175
NA.16: 6 residues within 4Å:- Chain C: D.127, A.129, D.131, S.175
- Ligands: LAF.13, LAF.14
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:D.127, C:S.175
NA.23: 4 residues within 4Å:- Chain D: D.127, S.175
- Ligands: LAF.18, LAF.19
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:D.127, D:S.175
NA.28: 6 residues within 4Å:- Chain E: D.127, A.129, D.131, S.175
- Ligands: LAF.25, LAF.26
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:S.175, E:S.175
NA.35: 4 residues within 4Å:- Chain F: D.127, S.175
- Ligands: LAF.30, LAF.31
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:S.175, F:S.175
NA.40: 6 residues within 4Å:- Chain G: D.127, A.129, D.131, S.175
- Ligands: LAF.37, LAF.38
2 PLIP interactions:2 interactions with chain G- Hydrogen bonds: G:S.175, G:S.175
NA.47: 4 residues within 4Å:- Chain H: D.127, S.175
- Ligands: LAF.42, LAF.43
2 PLIP interactions:2 interactions with chain H- Hydrogen bonds: H:D.127, H:S.175
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 4 residues within 4Å:- Chain A: F.119, P.120, E.121, L.122
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.121, A:L.122
- Water bridges: A:R.118
SO4.12: 5 residues within 4Å:- Chain B: V.76, F.119, P.120, E.121, L.122
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.121, B:L.122
SO4.17: 4 residues within 4Å:- Chain C: F.119, P.120, E.121, L.122
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:E.121, C:L.122
- Water bridges: C:R.118
SO4.24: 5 residues within 4Å:- Chain D: V.76, F.119, P.120, E.121, L.122
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.121, D:L.122
SO4.29: 4 residues within 4Å:- Chain E: F.119, P.120, E.121, L.122
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:E.121, E:L.122
- Water bridges: E:R.118
SO4.36: 5 residues within 4Å:- Chain F: V.76, F.119, P.120, E.121, L.122
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:E.121, F:L.122
SO4.41: 4 residues within 4Å:- Chain G: F.119, P.120, E.121, L.122
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:E.121, G:L.122
- Water bridges: G:R.118
SO4.48: 5 residues within 4Å:- Chain H: V.76, F.119, P.120, E.121, L.122
2 PLIP interactions:2 interactions with chain H- Hydrogen bonds: H:E.121, H:L.122
- 8 x K: POTASSIUM ION(Non-covalent)
K.8: 5 residues within 4Å:- Chain B: D.36, D.37, D.319
- Chain E: R.26, L.27
5 PLIP interactions:1 interactions with chain E, 2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: E:L.27, B:D.37, B:D.319, H2O.54, H2O.54
K.9: 6 residues within 4Å:- Chain B: R.26, L.27, R.29
- Chain E: D.36, D.37, D.319
5 PLIP interactions:1 interactions with chain B, 2 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: B:L.27, E:D.37, E:D.319, H2O.17, H2O.17
K.20: 5 residues within 4Å:- Chain A: R.26, L.27
- Chain D: D.36, D.37, D.319
5 PLIP interactions:1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: A:L.27, D:D.37, D:D.319, H2O.2, H2O.2
K.21: 6 residues within 4Å:- Chain A: D.36, D.37, D.319
- Chain D: R.26, L.27, R.29
5 PLIP interactions:2 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: A:D.37, A:D.319, D:L.27, H2O.42, H2O.42
K.32: 5 residues within 4Å:- Chain F: D.36, D.37, D.319
- Chain G: R.26, L.27
5 PLIP interactions:2 interactions with chain F, 1 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: F:D.37, F:D.319, G:L.27, H2O.80, H2O.80
K.33: 6 residues within 4Å:- Chain F: R.26, L.27, R.29
- Chain G: D.36, D.37, D.319
5 PLIP interactions:1 interactions with chain F, 2 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: F:L.27, G:D.37, G:D.319, H2O.68, H2O.68
K.44: 5 residues within 4Å:- Chain C: R.26, L.27
- Chain H: D.36, D.37, D.319
5 PLIP interactions:1 interactions with chain C, 2 interactions with chain H, 2 Ligand-Water interactions- Metal complexes: C:L.27, H:D.37, H:D.319, H2O.28, H2O.28
K.45: 6 residues within 4Å:- Chain C: D.36, D.37, D.319
- Chain H: R.26, L.27, R.29
5 PLIP interactions:2 interactions with chain C, 1 interactions with chain H, 2 Ligand-Water interactions- Metal complexes: C:D.37, C:D.319, H:L.27, H2O.94, H2O.94
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Frere, F. et al., Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism. J. Mol. Biol. (2002)
- Release Date
- 2002-06-27
- Peptides
- DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
BG
AH
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.66 Å
- Oligo State
- homo-octamer
- Ligands
- 16 x LAF: 5-FLUOROLEVULINIC ACID(Covalent)(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x NA: SODIUM ION(Non-functional Binders)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 8 x K: POTASSIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Frere, F. et al., Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism. J. Mol. Biol. (2002)
- Release Date
- 2002-06-27
- Peptides
- DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
BG
AH
B