- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.2: 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.10, H2O.10, H2O.11
MG.4: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.5: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.8: 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.22, H2O.23, H2O.23
MG.9: 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.33, H2O.34, H2O.34, H2O.34
MG.15: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.16: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.19: 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.46, H2O.46, H2O.46
MG.20: 1 residues within 4Å:- Chain D: N.49
No protein-ligand interaction detected (PLIP)MG.24: 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.56, H2O.56, H2O.58, H2O.58, H2O.58
MG.26: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.27: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.30: 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.70, H2O.70, H2O.70
MG.31: 1 residues within 4Å:- Chain F: N.49
No protein-ligand interaction detected (PLIP)MG.35: 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.80, H2O.80, H2O.82, H2O.82, H2O.82
MG.37: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.38: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.41: 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.92, H2O.92, H2O.94, H2O.94, H2O.94
MG.42: 1 residues within 4Å:- Chain H: N.49
No protein-ligand interaction detected (PLIP)- 8 x ZN: ZINC ION(Non-covalent)
ZN.3: 3 residues within 4Å:- Chain A: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:C.129, A:C.131, A:C.139, H2O.12
ZN.10: 3 residues within 4Å:- Chain B: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.129, B:C.131, B:C.139, H2O.24
ZN.14: 3 residues within 4Å:- Chain C: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:C.129, C:C.131, C:C.139, H2O.36
ZN.21: 3 residues within 4Å:- Chain D: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:C.129, D:C.131, D:C.139, H2O.48
ZN.25: 3 residues within 4Å:- Chain E: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:C.129, E:C.131, E:C.139, H2O.60
ZN.32: 3 residues within 4Å:- Chain F: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.129, F:C.131, F:C.139, H2O.72
ZN.36: 3 residues within 4Å:- Chain G: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain G, 1 Ligand-Water interactions- Metal complexes: G:C.129, G:C.131, G:C.139, H2O.84
ZN.43: 3 residues within 4Å:- Chain H: C.129, C.131, C.139
4 PLIP interactions:3 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: H:C.129, H:C.131, H:C.139, H2O.96
- 8 x NA: SODIUM ION(Non-functional Binders)
NA.6: 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.319
NA.11: 3 residues within 4Å:- Chain B: L.27
- Chain E: D.37, D.319
3 PLIP interactions:2 interactions with chain E, 1 interactions with chain B- Hydrogen bonds: E:D.37, B:R.29
- Water bridges: E:T.34
NA.17: 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.319
NA.22: 3 residues within 4Å:- Chain A: D.37, D.319
- Chain D: L.27
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.37, A:D.319
- Water bridges: A:T.34
NA.28: 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.319
NA.33: 3 residues within 4Å:- Chain F: L.27
- Chain G: D.37, D.319
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:D.37, G:D.37
- Water bridges: G:T.34
NA.39: 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.319
NA.44: 3 residues within 4Å:- Chain C: D.37, D.319
- Chain H: L.27
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain H- Hydrogen bonds: C:D.37, H:R.29
- Water bridges: C:T.34
- 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 1.40 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 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