- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 72 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 33 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.3: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.41, SO4.79
Ligand excluded by PLIPSO4.12: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.13: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.14: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.26: 7 residues within 4Å:- Chain C: H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.27: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.28: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.66, SO4.104
Ligand excluded by PLIPSO4.36: 3 residues within 4Å:- Chain F: S.204, I.205
- Ligands: EDO.59
Ligand excluded by PLIPSO4.37: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.38: 7 residues within 4Å:- Chain B: S.67, G.68, T.69
- Chain C: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.40: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.41: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.3, SO4.79
Ligand excluded by PLIPSO4.50: 2 residues within 4Å:- Chain E: L.108, R.112
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 PLIPSO4.64: 7 residues within 4Å:- Chain F: H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.65: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.66: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.28, SO4.104
Ligand excluded by PLIPSO4.74: 3 residues within 4Å:- Chain I: S.204, I.205
- Ligands: EDO.97
Ligand excluded by PLIPSO4.75: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.76: 7 residues within 4Å:- Chain E: S.67, G.68, T.69
- Chain F: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.78: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.79: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.3, SO4.41
Ligand excluded by PLIPSO4.88: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.89: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.90: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.102: 7 residues within 4Å:- Chain I: H.222, E.223, D.224, H.249, G.280, H.323, R.339
Ligand excluded by PLIPSO4.103: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.104: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.28, SO4.66
Ligand excluded by PLIPSO4.112: 3 residues within 4Å:- Chain C: S.204, I.205
- Ligands: EDO.21
Ligand excluded by PLIPSO4.113: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.114: 7 residues within 4Å:- Chain H: S.67, G.68, T.69
- Chain I: S.11, Y.12, N.43, K.48
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.15: 7 residues within 4Å:- Chain C: 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.9, 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.9, OH.17
NI.53: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.54, OH.55
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.37, OH.55
NI.54: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.53, OH.55
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.37, OH.55
NI.91: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.92, OH.93
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.64, OH.93
NI.92: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.91, OH.93
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.64, OH.93
- 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.55: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.53, NI.54
No protein-ligand interaction detected (PLIP)OH.93: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.91, NI.92
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 1.50 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 72 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 33 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