- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.07 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 27 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 PLIPSO4.4: 2 residues within 4Å:- Chain B: L.112, R.116
Ligand excluded by PLIPSO4.15: 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 PLIPSO4.17: 3 residues within 4Å:- Chain C: K.33, Y.35
- Ligands: EDO.13
Ligand excluded by PLIPSO4.18: 1 residues within 4Å:- Ligands: EDO.9
Ligand excluded by PLIPSO4.21: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.22: 4 residues within 4Å:- Chain C: M.106, D.107, G.108, V.109
Ligand excluded by PLIPSO4.23: 7 residues within 4Å:- Chain B: S.71, G.72, T.73
- Chain C: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.24: 2 residues within 4Å:- Chain C: R.388
- Ligands: HQE.19
Ligand excluded by PLIPSO4.26: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.28: 2 residues within 4Å:- Chain E: L.112, R.116
Ligand excluded by PLIPSO4.39: 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 PLIPSO4.41: 3 residues within 4Å:- Chain F: K.33, Y.35
- Ligands: EDO.37
Ligand excluded by PLIPSO4.42: 1 residues within 4Å:- Ligands: EDO.33
Ligand excluded by PLIPSO4.45: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.46: 4 residues within 4Å:- Chain F: M.106, D.107, G.108, V.109
Ligand excluded by PLIPSO4.47: 7 residues within 4Å:- Chain E: S.71, G.72, T.73
- Chain F: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.48: 2 residues within 4Å:- Chain F: R.388
- Ligands: HQE.43
Ligand excluded by PLIPSO4.50: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.52: 2 residues within 4Å:- Chain H: L.112, R.116
Ligand excluded by PLIPSO4.63: 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 PLIPSO4.65: 3 residues within 4Å:- Chain I: K.33, Y.35
- Ligands: EDO.61
Ligand excluded by PLIPSO4.66: 1 residues within 4Å:- Ligands: EDO.57
Ligand excluded by PLIPSO4.69: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.70: 4 residues within 4Å:- Chain I: M.106, D.107, G.108, V.109
Ligand excluded by PLIPSO4.71: 7 residues within 4Å:- Chain H: S.71, G.72, T.73
- Chain I: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.72: 2 residues within 4Å:- Chain I: R.388
- Ligands: HQE.67
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.5: 8 residues within 4Å:- Chain C: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.6, OH.16
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.11, OH.16
NI.6: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.5, OH.16
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.10, OH.16
NI.29: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.30, OH.40
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.40
NI.30: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.29, OH.40
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.28, OH.40
NI.53: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.54, OH.64
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.47, OH.64
NI.54: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.53, OH.64
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.46, OH.64
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.16: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.5, NI.6
No protein-ligand interaction detected (PLIP)OH.40: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.29, NI.30
No protein-ligand interaction detected (PLIP)OH.64: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.53, NI.54
No protein-ligand interaction detected (PLIP)- 6 x HQE: benzene-1,4-diol(Covalent)
HQE.19: 7 residues within 4Å:- Chain C: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.24
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:I.350, C:Q.387
- Hydrogen bonds: C:R.388, C:E.556, C:E.556
HQE.20: 6 residues within 4Å:- Chain C: V.321, C.322
- Chain D: Q.81
- Chain F: I.468, P.469, T.470
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain F- Hydrogen bonds: C:V.321, F:T.470
- Water bridges: C:K.169
- Hydrophobic interactions: F:I.468, F:I.468, F:T.470
HQE.43: 7 residues within 4Å:- Chain F: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.48
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:I.350, F:Q.387
- Hydrogen bonds: F:R.388, F:E.556, F:E.556
HQE.44: 6 residues within 4Å:- Chain F: V.321, C.322
- Chain G: Q.81
- Chain I: I.468, P.469, T.470
6 PLIP interactions:2 interactions with chain F, 4 interactions with chain I- Hydrogen bonds: F:V.321, I:T.470
- Water bridges: F:K.169
- Hydrophobic interactions: I:I.468, I:I.468, I:T.470
HQE.67: 7 residues within 4Å:- Chain I: I.350, Q.387, R.388, T.554, C.555, E.556
- Ligands: SO4.72
5 PLIP interactions:5 interactions with chain I- Hydrophobic interactions: I:I.350, I:Q.387
- Hydrogen bonds: I:R.388, I:E.556, I:E.556
HQE.68: 6 residues within 4Å:- Chain A: Q.81
- Chain C: I.468, P.469, T.470
- Chain I: V.321, C.322
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain I- Hydrophobic interactions: C:I.468, C:I.468, C:T.470
- Hydrogen bonds: C:T.470, I:V.321
- Water bridges: I:K.169
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inactivation of Urease by 1,4-Benzoquinone: Chemistry at the Protein Surface. Dalton Trans (2016)
- Release Date
- 2016-03-23
- Peptides
- UREASE SUBUNIT GAMMA: ADG
UREASE SUBUNIT BETA: BEH
UREASE SUBUNIT ALPHA: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
AG
AB
BE
BH
BC
CF
CI
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.07 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 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)
- 6 x HQE: benzene-1,4-diol(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Inactivation of Urease by 1,4-Benzoquinone: Chemistry at the Protein Surface. Dalton Trans (2016)
- Release Date
- 2016-03-23
- Peptides
- UREASE SUBUNIT GAMMA: ADG
UREASE SUBUNIT BETA: BEH
UREASE SUBUNIT ALPHA: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
AG
AB
BE
BH
BC
CF
CI
C