- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-octamer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x FMT: FORMIC ACID(Non-functional Binders)
FMT.4: 6 residues within 4Å:- Chain A: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Y.283, A:Y.283, A:S.286, A:Y.324
FMT.12: 6 residues within 4Å:- Chain B: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.286
- Water bridges: B:K.260, B:K.260, B:Y.283
FMT.25: 6 residues within 4Å:- Chain C: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Y.283, C:Y.283, C:S.286, C:Y.324
FMT.33: 6 residues within 4Å:- Chain D: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:S.286
- Water bridges: D:K.260, D:K.260, D:Y.283
FMT.46: 6 residues within 4Å:- Chain E: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Y.283, E:Y.283, E:S.286, E:Y.324
FMT.54: 6 residues within 4Å:- Chain F: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:S.286
- Water bridges: F:K.260, F:K.260, F:Y.283
FMT.67: 6 residues within 4Å:- Chain G: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain G- Hydrogen bonds: G:Y.283, G:Y.283, G:S.286, G:Y.324
FMT.75: 6 residues within 4Å:- Chain H: Y.211, F.214, Y.283, V.285, S.286, Y.324
4 PLIP interactions:4 interactions with chain H- Hydrogen bonds: H:S.286
- Water bridges: H:K.260, H:K.260, H:Y.283
- 8 x K: POTASSIUM ION(Non-covalent)
K.5: 6 residues within 4Å:- Chain A: R.26, L.27
- Chain D: D.36, D.37, D.319
- Ligands: GOL.39
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain A- Metal complexes: D:D.37, A:R.26
K.13: 7 residues within 4Å:- Chain B: R.26, L.27, R.29
- Chain E: D.36, D.37, D.319
- Ligands: GOL.16
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain E- Metal complexes: B:R.26, E:D.37
K.26: 6 residues within 4Å:- Chain C: R.26, L.27
- Chain H: D.36, D.37, D.319
- Ligands: GOL.81
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain H- Metal complexes: C:R.26, H:D.37
K.34: 7 residues within 4Å:- Chain A: D.36, D.37, D.319
- Chain D: R.26, L.27, R.29
- Ligands: GOL.37
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain A- Metal complexes: D:R.26, A:D.37
K.47: 6 residues within 4Å:- Chain B: D.36, D.37, D.319
- Chain E: R.26, L.27
- Ligands: GOL.18
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain E- Metal complexes: B:D.37, E:R.26
K.55: 7 residues within 4Å:- Chain F: R.26, L.27, R.29
- Chain G: D.36, D.37, D.319
- Ligands: GOL.58
2 PLIP interactions:1 interactions with chain G, 1 interactions with chain F- Metal complexes: G:D.37, F:R.26
K.68: 6 residues within 4Å:- Chain F: D.36, D.37, D.319
- Chain G: R.26, L.27
- Ligands: GOL.60
2 PLIP interactions:1 interactions with chain G, 1 interactions with chain F- Metal complexes: G:R.26, F:D.37
K.76: 7 residues within 4Å:- Chain C: D.36, D.37, D.319
- Chain H: R.26, L.27, R.29
- Ligands: GOL.79
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain H- Metal complexes: C:D.37, H:R.26
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.6: 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.7, H2O.7, H2O.9, H2O.9, H2O.9
MG.14: 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.18, H2O.18, H2O.19, H2O.19, H2O.19
MG.27: 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.27, H2O.28, H2O.29, H2O.29, H2O.29
MG.35: 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.38, H2O.38, H2O.39, H2O.39, H2O.39
MG.48: 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.48, H2O.48, H2O.49, H2O.49, H2O.49
MG.56: 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.58, H2O.59, H2O.60, H2O.60, H2O.60
MG.69: 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.68, H2O.68, H2O.70, H2O.70, H2O.70
MG.77: 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.79, H2O.79, H2O.80, H2O.80, H2O.80
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 2 residues within 4Å:- Chain A: R.20
- Chain D: N.196
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain D- Salt bridges: A:R.20
- Water bridges: D:N.196
SO4.15: 3 residues within 4Å:- Chain A: D.143
- Chain B: R.20
- Chain E: N.196
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain E- Water bridges: B:R.20, B:R.20, E:N.196, E:N.196
- Salt bridges: B:R.20
- Hydrogen bonds: E:N.196
SO4.28: 2 residues within 4Å:- Chain C: R.20
- Chain H: N.196
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain H- Salt bridges: C:R.20
- Water bridges: H:N.196
SO4.36: 3 residues within 4Å:- Chain A: N.196
- Chain C: D.143
- Chain D: R.20
6 PLIP interactions:3 interactions with chain A, 3 interactions with chain D- Hydrogen bonds: A:N.196
- Water bridges: A:N.196, A:N.196, D:R.20, D:R.20
- Salt bridges: D:R.20
SO4.49: 2 residues within 4Å:- Chain B: N.196
- Chain E: R.20
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain E- Water bridges: B:N.196
- Salt bridges: E:R.20
SO4.57: 3 residues within 4Å:- Chain E: D.143
- Chain F: R.20
- Chain G: N.196
6 PLIP interactions:3 interactions with chain G, 3 interactions with chain F- Hydrogen bonds: G:N.196
- Water bridges: G:N.196, G:N.196, F:R.20, F:R.20
- Salt bridges: F:R.20
SO4.70: 2 residues within 4Å:- Chain F: N.196
- Chain G: R.20
2 PLIP interactions:1 interactions with chain G, 1 interactions with chain F- Salt bridges: G:R.20
- Water bridges: F:N.196
SO4.78: 3 residues within 4Å:- Chain C: N.196
- Chain G: D.143
- Chain H: R.20
6 PLIP interactions:3 interactions with chain H, 3 interactions with chain C- Water bridges: H:R.20, H:R.20, C:N.196, C:N.196
- Salt bridges: H:R.20
- Hydrogen bonds: C:N.196
- 24 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 6 residues within 4Å:- Chain A: P.41, V.42, G.59, V.60, E.61, Y.324
Ligand excluded by PLIPGOL.16: 8 residues within 4Å:- Chain B: R.29, E.30, V.32
- Chain E: T.34, D.36, D.37, K.314
- Ligands: K.13
Ligand excluded by PLIPGOL.17: 5 residues within 4Å:- Chain B: P.41, V.42, V.60, E.61, W.75
Ligand excluded by PLIPGOL.18: 8 residues within 4Å:- Chain B: T.34, D.36, D.37, K.314
- Chain E: R.29, E.30, N.31
- Ligands: K.47
Ligand excluded by PLIPGOL.19: 6 residues within 4Å:- Chain A: R.29, E.308, T.311
- Chain B: D.235, P.236, A.237
Ligand excluded by PLIPGOL.20: 3 residues within 4Å:- Chain B: Q.138, N.228, K.229
Ligand excluded by PLIPGOL.29: 6 residues within 4Å:- Chain C: P.41, V.42, G.59, V.60, E.61, Y.324
Ligand excluded by PLIPGOL.37: 8 residues within 4Å:- Chain A: T.34, D.36, D.37, K.314
- Chain D: R.29, E.30, V.32
- Ligands: K.34
Ligand excluded by PLIPGOL.38: 5 residues within 4Å:- Chain D: P.41, V.42, V.60, E.61, W.75
Ligand excluded by PLIPGOL.39: 8 residues within 4Å:- Chain A: R.29, E.30, N.31
- Chain D: T.34, D.36, D.37, K.314
- Ligands: K.5
Ligand excluded by PLIPGOL.40: 6 residues within 4Å:- Chain C: R.29, E.308, T.311
- Chain D: D.235, P.236, A.237
Ligand excluded by PLIPGOL.41: 3 residues within 4Å:- Chain D: Q.138, N.228, K.229
Ligand excluded by PLIPGOL.50: 6 residues within 4Å:- Chain E: P.41, V.42, G.59, V.60, E.61, Y.324
Ligand excluded by PLIPGOL.58: 8 residues within 4Å:- Chain F: R.29, E.30, V.32
- Chain G: T.34, D.36, D.37, K.314
- Ligands: K.55
Ligand excluded by PLIPGOL.59: 5 residues within 4Å:- Chain F: P.41, V.42, V.60, E.61, W.75
Ligand excluded by PLIPGOL.60: 8 residues within 4Å:- Chain F: T.34, D.36, D.37, K.314
- Chain G: R.29, E.30, N.31
- Ligands: K.68
Ligand excluded by PLIPGOL.61: 6 residues within 4Å:- Chain E: R.29, E.308, T.311
- Chain F: D.235, P.236, A.237
Ligand excluded by PLIPGOL.62: 3 residues within 4Å:- Chain F: Q.138, N.228, K.229
Ligand excluded by PLIPGOL.71: 6 residues within 4Å:- Chain G: P.41, V.42, G.59, V.60, E.61, Y.324
Ligand excluded by PLIPGOL.79: 8 residues within 4Å:- Chain C: T.34, D.36, D.37, K.314
- Chain H: R.29, E.30, V.32
- Ligands: K.76
Ligand excluded by PLIPGOL.80: 5 residues within 4Å:- Chain H: P.41, V.42, V.60, E.61, W.75
Ligand excluded by PLIPGOL.81: 8 residues within 4Å:- Chain C: R.29, E.30, N.31
- Chain H: T.34, D.36, D.37, K.314
- Ligands: K.26
Ligand excluded by PLIPGOL.82: 6 residues within 4Å:- Chain G: R.29, E.308, T.311
- Chain H: D.235, P.236, A.237
Ligand excluded by PLIPGOL.83: 3 residues within 4Å:- Chain H: Q.138, N.228, K.229
Ligand excluded by PLIP- 8 x ZN: ZINC ION(Non-covalent)
ZN.9: 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.11
ZN.21: 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.21
ZN.30: 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.31
ZN.42: 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.41
ZN.51: 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.52
ZN.63: 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.62
ZN.72: 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.72
ZN.84: 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.82
- 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 1.55 Å
- Oligo State
- homo-octamer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 8 x K: POTASSIUM ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 24 x GOL: GLYCEROL(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