- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.61 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 87 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 45 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 1 residues within 4Å:- Chain A: E.75
Ligand excluded by PLIPSO4.13: 4 residues within 4Å:- Chain B: T.25, I.26, R.27, D.54
Ligand excluded by PLIPSO4.14: 2 residues within 4Å:- Chain B: K.23, E.82
Ligand excluded by PLIPSO4.15: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.16: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.38: 8 residues within 4Å:- Chain B: S.67, G.68, T.69
- Chain C: S.11, Y.12, N.43, K.48
- Ligands: EDO.22
Ligand excluded by PLIPSO4.39: 3 residues within 4Å:- Chain C: K.33, Y.35
- Ligands: EDO.32
Ligand excluded by PLIPSO4.40: 2 residues within 4Å:- Chain C: K.518
- Ligands: EDO.24
Ligand excluded by PLIPSO4.41: 4 residues within 4Å:- Chain B: G.88
- Chain C: M.106, D.107, G.108
Ligand excluded by PLIPSO4.42: 5 residues within 4Å:- Chain C: K.33, Y.35, T.80, Y.83
- Ligands: EDO.32
Ligand excluded by PLIPSO4.43: 1 residues within 4Å:- Chain C: R.388
Ligand excluded by PLIPSO4.44: 3 residues within 4Å:- Chain C: R.234
- Chain H: D.97, N.100
Ligand excluded by PLIPSO4.45: 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 PLIPSO4.46: 4 residues within 4Å:- Chain C: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.47: 3 residues within 4Å:- Chain F: S.204, I.205, A.206
Ligand excluded by PLIPSO4.53: 1 residues within 4Å:- Chain D: E.75
Ligand excluded by PLIPSO4.60: 4 residues within 4Å:- Chain E: T.25, I.26, R.27, D.54
Ligand excluded by PLIPSO4.61: 2 residues within 4Å:- Chain E: K.23, E.82
Ligand excluded by PLIPSO4.62: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.63: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.85: 8 residues within 4Å:- Chain E: S.67, G.68, T.69
- Chain F: S.11, Y.12, N.43, K.48
- Ligands: EDO.69
Ligand excluded by PLIPSO4.86: 3 residues within 4Å:- Chain F: K.33, Y.35
- Ligands: EDO.79
Ligand excluded by PLIPSO4.87: 2 residues within 4Å:- Chain F: K.518
- Ligands: EDO.71
Ligand excluded by PLIPSO4.88: 4 residues within 4Å:- Chain E: G.88
- Chain F: M.106, D.107, G.108
Ligand excluded by PLIPSO4.89: 5 residues within 4Å:- Chain F: K.33, Y.35, T.80, Y.83
- Ligands: EDO.79
Ligand excluded by PLIPSO4.90: 1 residues within 4Å:- Chain F: R.388
Ligand excluded by PLIPSO4.91: 3 residues within 4Å:- Chain B: D.97, N.100
- Chain F: R.234
Ligand excluded by PLIPSO4.92: 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 PLIPSO4.93: 4 residues within 4Å:- Chain F: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.94: 3 residues within 4Å:- Chain I: S.204, I.205, A.206
Ligand excluded by PLIPSO4.100: 1 residues within 4Å:- Chain G: E.75
Ligand excluded by PLIPSO4.107: 4 residues within 4Å:- Chain H: T.25, I.26, R.27, D.54
Ligand excluded by PLIPSO4.108: 2 residues within 4Å:- Chain H: K.23, E.82
Ligand excluded by PLIPSO4.109: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.110: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.132: 8 residues within 4Å:- Chain H: S.67, G.68, T.69
- Chain I: S.11, Y.12, N.43, K.48
- Ligands: EDO.116
Ligand excluded by PLIPSO4.133: 3 residues within 4Å:- Chain I: K.33, Y.35
- Ligands: EDO.126
Ligand excluded by PLIPSO4.134: 2 residues within 4Å:- Chain I: K.518
- Ligands: EDO.118
Ligand excluded by PLIPSO4.135: 4 residues within 4Å:- Chain H: G.88
- Chain I: M.106, D.107, G.108
Ligand excluded by PLIPSO4.136: 5 residues within 4Å:- Chain I: K.33, Y.35, T.80, Y.83
- Ligands: EDO.126
Ligand excluded by PLIPSO4.137: 1 residues within 4Å:- Chain I: R.388
Ligand excluded by PLIPSO4.138: 3 residues within 4Å:- Chain E: D.97, N.100
- Chain I: R.234
Ligand excluded by PLIPSO4.139: 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 PLIPSO4.140: 4 residues within 4Å:- Chain I: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.141: 3 residues within 4Å:- Chain C: S.204, I.205, A.206
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.18: 7 residues within 4Å:- Chain C: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.19, OH.20
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.20
NI.19: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.18, OH.20
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.20
NI.65: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.66, OH.67
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.29, OH.67
NI.66: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.65, OH.67
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.29, OH.67
NI.112: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.113, OH.114
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.51, OH.114
NI.113: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.112, OH.114
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.51, OH.114
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.20: 7 residues within 4Å:- Chain C: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.18, NI.19
No protein-ligand interaction detected (PLIP)OH.67: 7 residues within 4Å:- Chain F: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.65, NI.66
No protein-ligand interaction detected (PLIP)OH.114: 7 residues within 4Å:- Chain I: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.112, NI.113
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 1.61 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 87 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 45 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