- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.89 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 81 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 27 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.12: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.13: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.14: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.35: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.74, SO4.113
Ligand excluded by PLIPSO4.36: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.37: 2 residues within 4Å:- Chain C: N.65
- Ligands: EDO.28
Ligand excluded by PLIPSO4.38: 8 residues within 4Å:- Chain C: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.39: 2 residues within 4Å:- Chain C: K.518
- Ligands: EDO.33
Ligand excluded by PLIPSO4.47: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.51: 3 residues within 4Å:- Chain E: T.25, I.26, R.27
Ligand excluded by PLIPSO4.52: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.53: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.74: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.35, SO4.113
Ligand excluded by PLIPSO4.75: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.76: 2 residues within 4Å:- Chain F: N.65
- Ligands: EDO.67
Ligand excluded by PLIPSO4.77: 8 residues within 4Å:- Chain F: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.78: 2 residues within 4Å:- Chain F: K.518
- Ligands: EDO.72
Ligand excluded by PLIPSO4.86: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.90: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.91: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.92: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.113: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.35, SO4.74
Ligand excluded by PLIPSO4.114: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.115: 2 residues within 4Å:- Chain I: N.65
- Ligands: EDO.106
Ligand excluded by PLIPSO4.116: 8 residues within 4Å:- Chain I: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.117: 2 residues within 4Å:- Chain I: K.518
- Ligands: EDO.111
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.15: 8 residues within 4Å:- Chain C: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.16, OH.17
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.7, OH.17
NI.16: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.15, OH.17
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.7, OH.17
NI.54: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.55, OH.56
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.30, OH.56
NI.55: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.54, OH.56
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.30, OH.56
NI.93: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.94, OH.95
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.52, OH.95
NI.94: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.93, OH.95
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.52, OH.95
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.17: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.15, NI.16
No protein-ligand interaction detected (PLIP)OH.56: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.54, NI.55
No protein-ligand interaction detected (PLIP)OH.95: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.93, NI.94
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 1.89 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 81 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 27 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