- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 18 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 2 residues within 4Å:- Chain B: I.26, R.27
Ligand excluded by PLIPSO4.8: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.26: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.27: 8 residues within 4Å:- Chain C: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.17
Ligand excluded by PLIPSO4.28: 3 residues within 4Å:- Chain C: S.204, I.205
- Ligands: EDO.15
Ligand excluded by PLIPSO4.29: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.36: 2 residues within 4Å:- Chain E: I.26, R.27
Ligand excluded by PLIPSO4.37: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.55: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.56: 8 residues within 4Å:- Chain F: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.46
Ligand excluded by PLIPSO4.57: 3 residues within 4Å:- Chain F: S.204, I.205
- Ligands: EDO.44
Ligand excluded by PLIPSO4.58: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.65: 2 residues within 4Å:- Chain H: I.26, R.27
Ligand excluded by PLIPSO4.66: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.84: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.85: 8 residues within 4Å:- Chain I: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.75
Ligand excluded by PLIPSO4.86: 3 residues within 4Å:- Chain I: S.204, I.205
- Ligands: EDO.73
Ligand excluded by PLIPSO4.87: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.9: 7 residues within 4Å:- Chain C: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.10, OH.11
4 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: C:H.249, C:H.275, H2O.10, OH.11
NI.10: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.9, OH.11
5 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: C:H.137, C:H.139, C:D.363, H2O.10, OH.11
NI.38: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.39, OH.40
4 PLIP interactions:2 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: F:H.249, F:H.275, H2O.39, OH.40
NI.39: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.38, OH.40
5 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: F:H.137, F:H.139, F:D.363, H2O.39, OH.40
NI.67: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.68, OH.69
4 PLIP interactions:2 interactions with chain I, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: I:H.249, I:H.275, H2O.68, OH.69
NI.68: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.67, OH.69
5 PLIP interactions:3 interactions with chain I, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: I:H.137, I:H.139, I:D.363, H2O.68, OH.69
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.11: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.9, NI.10
No protein-ligand interaction detected (PLIP)OH.40: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.38, NI.39
No protein-ligand interaction detected (PLIP)OH.69: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.67, NI.68
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew.Chem.Int.Ed.Engl. (2021)
- Release Date
- 2020-12-23
- Peptides
- Urease subunit gamma: ADG
Urease subunit beta: BEH
Urease subunit alpha: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AAAD
AAAG
AAAB
BBBE
BBBH
BBBC
CCCF
CCCI
CCC
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 18 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x OH: HYDROXIDE ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew.Chem.Int.Ed.Engl. (2021)
- Release Date
- 2020-12-23
- Peptides
- Urease subunit gamma: ADG
Urease subunit beta: BEH
Urease subunit alpha: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AAAD
AAAG
AAAB
BBBE
BBBH
BBBC
CCCF
CCCI
CCC