- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.2: 4 residues within 4Å:- Chain A: Y.147, N.150
- Chain E: T.195, N.196
Ligand excluded by PLIPCL.12: 4 residues within 4Å:- Chain A: T.195, N.196
- Chain C: Y.147, N.150
Ligand excluded by PLIPCL.22: 4 residues within 4Å:- Chain E: Y.147, N.150
- Chain G: T.195, N.196
Ligand excluded by PLIPCL.32: 4 residues within 4Å:- Chain C: T.195, N.196
- Chain G: Y.147, N.150
Ligand excluded by PLIP- 12 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.9, H2O.9, H2O.11, H2O.11, H2O.11
MG.7: 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.21, H2O.21, H2O.23, H2O.23, H2O.23
MG.8: 1 residues within 4Å:- Chain B: N.49
No protein-ligand interaction detected (PLIP)MG.13: 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.33, H2O.34, H2O.35, H2O.35, H2O.35
MG.17: 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.45, H2O.45, H2O.47, H2O.47, H2O.47
MG.18: 1 residues within 4Å:- Chain D: N.49
No protein-ligand interaction detected (PLIP)MG.23: 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.58, H2O.58, H2O.59, H2O.59, H2O.59
MG.27: 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.69, H2O.69, H2O.71, H2O.71, H2O.71
MG.28: 1 residues within 4Å:- Chain F: N.49
No protein-ligand interaction detected (PLIP)MG.33: 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.82, H2O.82, H2O.83, H2O.83, H2O.83
MG.37: 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.93, H2O.93, H2O.95, H2O.95, H2O.95
MG.38: 1 residues within 4Å:- Chain H: N.49
No protein-ligand interaction detected (PLIP)- 8 x ZN: ZINC ION(Non-covalent)
ZN.4: 3 residues within 4Å:- Chain A: A.129, C.131, C.139
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:C.131, A:C.139, H2O.9, H2O.13
ZN.9: 3 residues within 4Å:- Chain B: A.129, C.131, C.139
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.131, B:C.139, H2O.25
ZN.14: 3 residues within 4Å:- Chain C: A.129, C.131, C.139
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:C.131, C:C.139, H2O.33, H2O.37
ZN.19: 3 residues within 4Å:- Chain D: A.129, C.131, C.139
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:C.131, D:C.139, H2O.49
ZN.24: 3 residues within 4Å:- Chain E: A.129, C.131, C.139
4 PLIP interactions:2 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:C.131, E:C.139, H2O.57, H2O.61
ZN.29: 3 residues within 4Å:- Chain F: A.129, C.131, C.139
3 PLIP interactions:2 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.131, F:C.139, H2O.73
ZN.34: 3 residues within 4Å:- Chain G: A.129, C.131, C.139
4 PLIP interactions:2 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: G:C.131, G:C.139, H2O.81, H2O.85
ZN.39: 3 residues within 4Å:- Chain H: A.129, C.131, C.139
3 PLIP interactions:2 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: H:C.131, H:C.139, H2O.97
- 8 x NA: SODIUM ION(Non-functional Binders)
NA.5: 3 residues within 4Å:- Chain A: L.27
- Chain D: D.37, D.319
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:D.37
NA.10: 3 residues within 4Å:- Chain B: L.27
- Chain E: D.37, D.319
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain B- Hydrogen bonds: E:D.37, B:R.29
NA.15: 3 residues within 4Å:- Chain C: L.27
- Chain H: D.37, D.319
1 PLIP interactions:1 interactions with chain H- Hydrogen bonds: H:D.37
NA.20: 3 residues within 4Å:- Chain A: D.37, D.319
- Chain D: L.27
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:L.27, A:D.37
NA.25: 3 residues within 4Å:- Chain B: D.37, D.319
- Chain E: L.27
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.37
NA.30: 3 residues within 4Å:- Chain F: L.27
- Chain G: D.37, D.319
2 PLIP interactions:2 interactions with chain G- Hydrogen bonds: G:D.37, G:D.319
NA.35: 3 residues within 4Å:- Chain F: D.37, D.319
- Chain G: L.27
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:D.37
NA.40: 3 residues within 4Å:- Chain C: D.37, D.319
- Chain H: L.27
2 PLIP interactions:1 interactions with chain H, 1 interactions with chain C- Hydrogen bonds: H:L.27, C:D.37
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Frere, F. et al., Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro. J.Mol.Biol. (2005)
- Release Date
- 2005-01-19
- 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 1.65 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 12 x MG: MAGNESIUM ION(Non-covalent)
- 8 x ZN: ZINC ION(Non-covalent)
- 8 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Frere, F. et al., Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro. J.Mol.Biol. (2005)
- Release Date
- 2005-01-19
- Peptides
- DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
BG
AH
B