- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.91 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 18 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.6: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.7: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.17: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.18: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.19: 10 residues within 4Å:- Chain C: H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.11, AG.20, AG.21
Ligand excluded by PLIPSO4.25: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.27: 3 residues within 4Å:- Chain E: T.25, I.26, R.27
Ligand excluded by PLIPSO4.28: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.38: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.39: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.40: 10 residues within 4Å:- Chain F: H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.32, AG.41, AG.42
Ligand excluded by PLIPSO4.46: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.48: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.49: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.59: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.60: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.61: 10 residues within 4Å:- Chain I: H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.53, AG.62, AG.63
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.8: 8 residues within 4Å:- Chain C: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.9, OH.10
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.10
NI.9: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.8, OH.10
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.10
NI.29: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.30, OH.31
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.24, OH.31
NI.30: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.29, OH.31
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.24, OH.31
NI.50: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.51, OH.52
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.43, OH.52
NI.51: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.50, OH.52
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.43, OH.52
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.10: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.8, NI.9
No protein-ligand interaction detected (PLIP)OH.31: 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.52: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.50, NI.51
No protein-ligand interaction detected (PLIP)- 6 x AG: SILVER ION(Non-covalent)
AG.20: 5 residues within 4Å:- Chain C: C.322, H.323
- Ligands: EDO.11, SO4.19, AG.21
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:C.322, C:H.323
AG.21: 5 residues within 4Å:- Chain C: C.322, R.339, M.367
- Ligands: SO4.19, AG.20
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:C.322, H2O.16
AG.41: 5 residues within 4Å:- Chain F: C.322, H.323
- Ligands: EDO.32, SO4.40, AG.42
2 PLIP interactions:2 interactions with chain F- Metal complexes: F:C.322, F:H.323
AG.42: 5 residues within 4Å:- Chain F: C.322, R.339, M.367
- Ligands: SO4.40, AG.41
2 PLIP interactions:1 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.322, H2O.34
AG.62: 5 residues within 4Å:- Chain I: C.322, H.323
- Ligands: EDO.53, SO4.61, AG.63
2 PLIP interactions:2 interactions with chain I- Metal complexes: I:C.322, I:H.323
AG.63: 5 residues within 4Å:- Chain I: C.322, R.339, M.367
- Ligands: SO4.61, AG.62
2 PLIP interactions:1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: I:C.322, H2O.53
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals. Dalton Trans (2018)
- Release Date
- 2019-01-16
- 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 1.91 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 18 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x OH: HYDROXIDE ION(Non-covalent)
- 6 x AG: SILVER ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals. Dalton Trans (2018)
- Release Date
- 2019-01-16
- 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