- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x CL: CHLORIDE ION(Non-functional Binders)
- 8 x FMT: FORMIC ACID(Non-functional Binders)
FMT.3: 6 residues within 4Å:- Chain A: Y.211, F.214, Y.283, V.285, S.286, Y.324
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.283, A:S.286, A:Y.324
FMT.8: 6 residues within 4Å:- Chain B: Y.211, F.214, Y.283, V.285, S.286, Y.324
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.286
FMT.16: 6 residues within 4Å:- Chain C: Y.211, F.214, Y.283, V.285, S.286, Y.324
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Y.283, C:S.286, C:Y.324
FMT.21: 6 residues within 4Å:- Chain D: Y.211, F.214, Y.283, V.285, S.286, Y.324
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:S.286
FMT.29: 6 residues within 4Å:- Chain E: Y.211, F.214, Y.283, V.285, S.286, Y.324
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:Y.283, E:S.286, E:Y.324
FMT.34: 6 residues within 4Å:- Chain F: Y.211, F.214, Y.283, V.285, S.286, Y.324
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:S.286
FMT.42: 6 residues within 4Å:- Chain G: Y.211, F.214, Y.283, V.285, S.286, Y.324
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:Y.283, G:S.286, G:Y.324
FMT.47: 6 residues within 4Å:- Chain H: Y.211, F.214, Y.283, V.285, S.286, Y.324
1 PLIP interactions:1 interactions with chain H- Hydrogen bonds: H:S.286
- 28 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.4: 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.13, H2O.13, H2O.15, H2O.15, H2O.15
MG.6: 2 residues within 4Å:- Chain D: D.37, D.319
6 PLIP interactions:2 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:D.37, D:D.319, H2O.3, H2O.55, H2O.56, H2O.68
MG.7: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.9: 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.30, H2O.30, H2O.32, H2O.32, H2O.32
MG.10: 2 residues within 4Å:- Chain B: N.49, Q.67
No protein-ligand interaction detected (PLIP)MG.12: 3 residues within 4Å:- Chain B: L.27
- Chain E: D.37, D.319
6 PLIP interactions:2 interactions with chain E, 4 Ligand-Water interactions- Metal complexes: E:D.37, E:D.319, H2O.20, H2O.72, H2O.73, H2O.85
MG.13: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.17: 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.47, H2O.47, H2O.49, H2O.49, H2O.49
MG.19: 2 residues within 4Å:- Chain H: D.37, D.319
6 PLIP interactions:2 interactions with chain H, 4 Ligand-Water interactions- Metal complexes: H:D.37, H:D.319, H2O.37, H2O.124, H2O.124, H2O.136
MG.20: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)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.64, H2O.64, H2O.66, H2O.66, H2O.66
MG.23: 2 residues within 4Å:- Chain D: N.49, Q.67
No protein-ligand interaction detected (PLIP)MG.25: 3 residues within 4Å:- Chain A: D.37, D.319
- Chain D: L.27
6 PLIP interactions:2 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.37, A:D.319, H2O.4, H2O.4, H2O.17, H2O.54
MG.26: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.30: 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.81, H2O.81, H2O.83, H2O.83, H2O.83
MG.32: 2 residues within 4Å:- Chain B: D.37, D.319
6 PLIP interactions:2 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.37, B:D.319, H2O.21, H2O.22, H2O.34, H2O.71
MG.33: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.35: 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.98, H2O.98, H2O.100, H2O.100, H2O.100
MG.36: 2 residues within 4Å:- Chain F: N.49, Q.67
No protein-ligand interaction detected (PLIP)MG.38: 3 residues within 4Å:- Chain F: L.27
- Chain G: D.37, D.319
6 PLIP interactions:2 interactions with chain G, 4 Ligand-Water interactions- Metal complexes: G:D.37, G:D.319, H2O.89, H2O.107, H2O.107, H2O.119
MG.39: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.43: 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.115, H2O.115, H2O.117, H2O.117, H2O.117
MG.45: 2 residues within 4Å:- Chain F: D.37, D.319
6 PLIP interactions:2 interactions with chain F, 4 Ligand-Water interactions- Metal complexes: F:D.37, F:D.319, H2O.90, H2O.90, H2O.102, H2O.105
MG.46: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.48: 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.133, H2O.133, H2O.134, H2O.134, H2O.134
MG.49: 2 residues within 4Å:- Chain H: N.49, Q.67
No protein-ligand interaction detected (PLIP)MG.51: 3 residues within 4Å:- Chain C: D.37, D.319
- Chain H: L.27
6 PLIP interactions:2 interactions with chain C, 4 Ligand-Water interactions- Metal complexes: C:D.37, C:D.319, H2O.38, H2O.38, H2O.51, H2O.123
MG.52: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 8 x ZN: ZINC ION(Non-covalent)
ZN.5: 3 residues within 4Å:- Chain A: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:C.129, A:D.131, A:C.139, H2O.17
ZN.11: 3 residues within 4Å:- Chain B: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.129, B:D.131, B:C.139, H2O.35
ZN.18: 3 residues within 4Å:- Chain C: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:C.129, C:D.131, C:C.139, H2O.52
ZN.24: 3 residues within 4Å:- Chain D: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:C.129, D:D.131, D:C.139, H2O.69
ZN.31: 3 residues within 4Å:- Chain E: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:C.129, E:D.131, E:C.139, H2O.86
ZN.37: 3 residues within 4Å:- Chain F: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.129, F:D.131, F:C.139, H2O.103
ZN.44: 3 residues within 4Å:- Chain G: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain G, 1 Ligand-Water interactions- Metal complexes: G:C.129, G:D.131, G:C.139, H2O.120
ZN.50: 3 residues within 4Å:- Chain H: C.129, D.131, C.139
4 PLIP interactions:3 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: H:C.129, H:D.131, H:C.139, H2O.137
- 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 1.60 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x CL: CHLORIDE ION(Non-functional Binders)
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 28 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 8 x ZN: ZINC ION(Non-covalent)
- 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