- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.63 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 51 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.7: 3 residues within 4Å:- Chain A: F.42, E.59, H.62
Ligand excluded by PLIPSO4.8: 2 residues within 4Å:- Chain A: N.97
- Chain F: K.326
Ligand excluded by PLIPSO4.9: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.10: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.11: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.12: 6 residues within 4Å:- Chain A: E.75
- Chain B: V.4, P.5, G.6, E.7
- Chain C: K.441
Ligand excluded by PLIPSO4.13: 2 residues within 4Å:- Chain B: K.23, E.82
Ligand excluded by PLIPSO4.14: 4 residues within 4Å:- Chain B: T.25, E.80, V.81, E.82
Ligand excluded by PLIPSO4.35: 2 residues within 4Å:- Chain C: R.388
- Ligands: HQE.34
Ligand excluded by PLIPSO4.36: 4 residues within 4Å:- Chain C: K.33, D.34, Y.35
- Ligands: EDO.31
Ligand excluded by PLIPSO4.37: 2 residues within 4Å:- Chain C: K.518
- Ligands: EDO.29
Ligand excluded by PLIPSO4.38: 2 residues within 4Å:- Chain C: S.204, I.205
Ligand excluded by PLIPSO4.39: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.40: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.82, SO4.124
Ligand excluded by PLIPSO4.41: 4 residues within 4Å:- Chain C: K.185, K.507, L.508, G.509
Ligand excluded by PLIPSO4.42: 8 residues within 4Å:- Chain C: A.170, H.222, E.223, D.224, H.249, H.323, R.339
- Ligands: EDO.24
Ligand excluded by PLIPSO4.48: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.49: 3 residues within 4Å:- Chain D: F.42, E.59, H.62
Ligand excluded by PLIPSO4.50: 2 residues within 4Å:- Chain D: N.97
- Chain I: K.326
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 PLIPSO4.54: 6 residues within 4Å:- Chain D: E.75
- Chain E: V.4, P.5, G.6, E.7
- Chain F: K.441
Ligand excluded by PLIPSO4.55: 2 residues within 4Å:- Chain E: K.23, E.82
Ligand excluded by PLIPSO4.56: 4 residues within 4Å:- Chain E: T.25, E.80, V.81, E.82
Ligand excluded by PLIPSO4.77: 2 residues within 4Å:- Chain F: R.388
- Ligands: HQE.76
Ligand excluded by PLIPSO4.78: 4 residues within 4Å:- Chain F: K.33, D.34, Y.35
- Ligands: EDO.73
Ligand excluded by PLIPSO4.79: 2 residues within 4Å:- Chain F: K.518
- Ligands: EDO.71
Ligand excluded by PLIPSO4.80: 2 residues within 4Å:- Chain F: S.204, I.205
Ligand excluded by PLIPSO4.81: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.82: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.40, SO4.124
Ligand excluded by PLIPSO4.83: 4 residues within 4Å:- Chain F: K.185, K.507, L.508, G.509
Ligand excluded by PLIPSO4.84: 8 residues within 4Å:- Chain F: A.170, H.222, E.223, D.224, H.249, H.323, R.339
- Ligands: EDO.66
Ligand excluded by PLIPSO4.90: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.91: 3 residues within 4Å:- Chain G: F.42, E.59, H.62
Ligand excluded by PLIPSO4.92: 2 residues within 4Å:- Chain C: K.326
- Chain G: N.97
Ligand excluded by PLIPSO4.93: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.94: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.95: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.96: 6 residues within 4Å:- Chain G: E.75
- Chain H: V.4, P.5, G.6, E.7
- Chain I: K.441
Ligand excluded by PLIPSO4.97: 2 residues within 4Å:- Chain H: K.23, E.82
Ligand excluded by PLIPSO4.98: 4 residues within 4Å:- Chain H: T.25, E.80, V.81, E.82
Ligand excluded by PLIPSO4.119: 2 residues within 4Å:- Chain I: R.388
- Ligands: HQE.118
Ligand excluded by PLIPSO4.120: 4 residues within 4Å:- Chain I: K.33, D.34, Y.35
- Ligands: EDO.115
Ligand excluded by PLIPSO4.121: 2 residues within 4Å:- Chain I: K.518
- Ligands: EDO.113
Ligand excluded by PLIPSO4.122: 2 residues within 4Å:- Chain I: S.204, I.205
Ligand excluded by PLIPSO4.123: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.124: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.40, SO4.82
Ligand excluded by PLIPSO4.125: 4 residues within 4Å:- Chain I: K.185, K.507, L.508, G.509
Ligand excluded by PLIPSO4.126: 8 residues within 4Å:- Chain I: A.170, H.222, E.223, D.224, H.249, H.323, R.339
- Ligands: EDO.108
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.57: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.58, OH.59
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.34, OH.59
NI.58: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.57, OH.59
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.34, OH.59
NI.99: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.100, OH.101
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.60, OH.101
NI.100: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.99, OH.101
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.60, OH.101
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.17: 7 residues within 4Å:- Chain C: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.15, NI.16
No protein-ligand interaction detected (PLIP)OH.59: 7 residues within 4Å:- Chain F: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.57, NI.58
No protein-ligand interaction detected (PLIP)OH.101: 7 residues within 4Å:- Chain I: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.99, NI.100
No protein-ligand interaction detected (PLIP)- 6 x HQE: benzene-1,4-diol(Covalent)
HQE.33: 7 residues within 4Å:- Chain C: K.169, V.321, C.322
- Chain G: Q.81
- Chain I: I.468, P.469, T.470
8 PLIP interactions:4 interactions with chain I, 1 interactions with chain G, 3 interactions with chain C- Hydrophobic interactions: I:I.468, I:I.468, I:T.470
- Hydrogen bonds: I:T.470, G:Q.81
- Water bridges: C:K.169, C:K.169, C:A.366
HQE.34: 7 residues within 4Å:- Chain C: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.35
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.350
- Hydrogen bonds: C:E.556
- Water bridges: C:Q.387
HQE.75: 7 residues within 4Å:- Chain A: Q.81
- Chain C: I.468, P.469, T.470
- Chain F: K.169, V.321, C.322
8 PLIP interactions:4 interactions with chain C, 3 interactions with chain F, 1 interactions with chain A- Hydrophobic interactions: C:I.468, C:I.468, C:T.470
- Hydrogen bonds: C:T.470, A:Q.81
- Water bridges: F:K.169, F:K.169, F:A.366
HQE.76: 7 residues within 4Å:- Chain F: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.77
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:I.350
- Hydrogen bonds: F:E.556
- Water bridges: F:Q.387
HQE.117: 7 residues within 4Å:- Chain D: Q.81
- Chain F: I.468, P.469, T.470
- Chain I: K.169, V.321, C.322
8 PLIP interactions:1 interactions with chain D, 3 interactions with chain I, 4 interactions with chain F- Hydrogen bonds: D:Q.81, F:T.470
- Water bridges: I:K.169, I:K.169, I:A.366
- Hydrophobic interactions: F:I.468, F:I.468, F:T.470
HQE.118: 7 residues within 4Å:- Chain I: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.119
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:I.350
- Hydrogen bonds: I:E.556
- Water bridges: I:Q.387
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study. Chemistry (2022)
- Release Date
- 2023-06-14
- 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 1.63 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 51 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x OH: HYDROXIDE ION(Non-covalent)
- 6 x HQE: benzene-1,4-diol(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study. Chemistry (2022)
- Release Date
- 2023-06-14
- 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