- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.23 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 66 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 27 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 PLIPSO4.9: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.29: 9 residues within 4Å:- Chain C: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.18, EDO.26
Ligand excluded by PLIPSO4.30: 4 residues within 4Å:- Chain C: V.558, K.559, E.560
- Ligands: EDO.22
Ligand excluded by PLIPSO4.31: 3 residues within 4Å:- Chain C: R.513, I.514
- Ligands: EDO.20
Ligand excluded by PLIPSO4.32: 3 residues within 4Å:- Chain C: T.59, Y.60, E.64
Ligand excluded by PLIPSO4.33: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.34: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.68, SO4.102
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain E: I.26, R.27
Ligand excluded by PLIPSO4.42: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.43: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.63: 9 residues within 4Å:- Chain F: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.52, EDO.60
Ligand excluded by PLIPSO4.64: 4 residues within 4Å:- Chain F: V.558, K.559, E.560
- Ligands: EDO.56
Ligand excluded by PLIPSO4.65: 3 residues within 4Å:- Chain F: R.513, I.514
- Ligands: EDO.54
Ligand excluded by PLIPSO4.66: 3 residues within 4Å:- Chain F: T.59, Y.60, E.64
Ligand excluded by PLIPSO4.67: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.68: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.34, SO4.102
Ligand excluded by PLIPSO4.75: 2 residues within 4Å:- Chain H: I.26, R.27
Ligand excluded by PLIPSO4.76: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.77: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.97: 9 residues within 4Å:- Chain I: H.222, E.223, D.224, H.249, G.280, H.323, R.339
- Ligands: EDO.86, EDO.94
Ligand excluded by PLIPSO4.98: 4 residues within 4Å:- Chain I: V.558, K.559, E.560
- Ligands: EDO.90
Ligand excluded by PLIPSO4.99: 3 residues within 4Å:- Chain I: R.513, I.514
- Ligands: EDO.88
Ligand excluded by PLIPSO4.100: 3 residues within 4Å:- Chain I: T.59, Y.60, E.64
Ligand excluded by PLIPSO4.101: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.102: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.34, SO4.68
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.10: 8 residues within 4Å:- Chain C: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.11, OH.12
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.6, OH.12
NI.11: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.10, OH.12
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.6, OH.12
NI.44: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.45, OH.46
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.21, OH.46
NI.45: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.44, OH.46
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.21, OH.46
NI.78: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.79, OH.80
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.36, OH.80
NI.79: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.78, OH.80
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.36, OH.80
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.12: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.10, NI.11
No protein-ligand interaction detected (PLIP)OH.46: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.44, NI.45
No protein-ligand interaction detected (PLIP)OH.80: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.78, NI.79
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 2.23 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 66 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