- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.97 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 39 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 30 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.6: 8 residues within 4Å:- Chain A: E.18
- Chain D: L.15, E.18
- Chain G: F.14, L.15, E.18
- Ligands: SO4.34, SO4.62
Ligand excluded by PLIPSO4.7: 3 residues within 4Å:- Chain B: T.25, 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 PLIPSO4.24: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.25: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.26: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.27: 11 residues within 4Å:- Chain C: A.170, H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.16, AG.18, AG.19
Ligand excluded by PLIPSO4.28: 3 residues within 4Å:- Chain C: H.293, P.294, N.295
Ligand excluded by PLIPSO4.33: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.34: 8 residues within 4Å:- Chain A: F.14, L.15, E.18
- Chain D: E.18
- Chain G: L.15, E.18
- Ligands: SO4.6, SO4.62
Ligand excluded by PLIPSO4.35: 3 residues within 4Å:- Chain E: T.25, I.26, R.27
Ligand excluded by PLIPSO4.36: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.37: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.52: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.53: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.54: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.55: 11 residues within 4Å:- Chain F: A.170, H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.44, AG.46, AG.47
Ligand excluded by PLIPSO4.56: 3 residues within 4Å:- Chain F: H.293, P.294, N.295
Ligand excluded by PLIPSO4.61: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.62: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: F.14, L.15, E.18
- Chain G: E.18
- Ligands: SO4.6, SO4.34
Ligand excluded by PLIPSO4.63: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.64: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.65: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.80: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.81: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.82: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.83: 11 residues within 4Å:- Chain I: A.170, H.222, E.223, H.249, G.280, H.323, R.339, M.367
- Ligands: EDO.72, AG.74, AG.75
Ligand excluded by PLIPSO4.84: 3 residues within 4Å:- Chain I: H.293, P.294, N.295
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, O.15
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, O.15
NI.11: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.10, O.15
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, O.15
NI.38: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.39, O.43
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.25, O.43
NI.39: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.38, O.43
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.25, O.43
NI.66: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.67, O.71
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, O.71
NI.67: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.66, O.71
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, O.71
- 3 x O: OXYGEN ATOM(Non-covalent)
O.15: 7 residues within 4Å:- Chain C: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.10, NI.11
No protein-ligand interaction detected (PLIP)O.43: 7 residues within 4Å:- Chain F: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.38, NI.39
No protein-ligand interaction detected (PLIP)O.71: 7 residues within 4Å:- Chain I: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.66, NI.67
No protein-ligand interaction detected (PLIP)- 6 x AG: SILVER ION(Non-covalent)
AG.18: 4 residues within 4Å:- Chain C: C.322, M.367
- Ligands: AG.19, SO4.27
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:C.322, H2O.16
AG.19: 5 residues within 4Å:- Chain C: C.322, H.323
- Ligands: EDO.16, AG.18, SO4.27
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:C.322, C:H.323
AG.46: 4 residues within 4Å:- Chain F: C.322, M.367
- Ligands: AG.47, SO4.55
2 PLIP interactions:1 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.322, H2O.34
AG.47: 5 residues within 4Å:- Chain F: C.322, H.323
- Ligands: EDO.44, AG.46, SO4.55
2 PLIP interactions:2 interactions with chain F- Metal complexes: F:C.322, F:H.323
AG.74: 4 residues within 4Å:- Chain I: C.322, M.367
- Ligands: AG.75, SO4.83
2 PLIP interactions:1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: I:C.322, H2O.52
AG.75: 5 residues within 4Å:- Chain I: C.322, H.323
- Ligands: EDO.72, AG.74, SO4.83
2 PLIP interactions:2 interactions with chain I- Metal complexes: I:C.322, I:H.323
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. J.Inorg.Biochem. (2021)
- Release Date
- 2021-10-13
- 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 1.97 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 39 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 30 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x O: OXYGEN ATOM(Non-covalent)
- 6 x AG: SILVER ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. J.Inorg.Biochem. (2021)
- Release Date
- 2021-10-13
- 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