- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 45 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: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.44, SO4.81
Ligand excluded by PLIPSO4.10: 2 residues within 4Å:- Chain B: I.26, R.27
Ligand excluded by PLIPSO4.11: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.12: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.26: 3 residues within 4Å:- Chain C: D.34, T.36, Y.38
Ligand excluded by PLIPSO4.27: 3 residues within 4Å:- Chain C: S.204, I.205, A.206
Ligand excluded by PLIPSO4.28: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.29: 4 residues within 4Å:- Chain C: Y.93, H.422, E.423, G.430
Ligand excluded by PLIPSO4.30: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
Ligand excluded by PLIPSO4.31: 12 residues within 4Å:- Chain C: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367
- Ligands: EDO.17, AG.20, AG.21
Ligand excluded by PLIPSO4.32: 2 residues within 4Å:- Chain C: T.470
- Chain F: H.324
Ligand excluded by PLIPSO4.33: 3 residues within 4Å:- Chain C: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.34: 4 residues within 4Å:- Chain C: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.35: 3 residues within 4Å:- Chain C: M.106, D.107, G.108
Ligand excluded by PLIPSO4.36: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.73, SO4.110
Ligand excluded by PLIPSO4.37: 4 residues within 4Å:- Chain C: E.343, E.542, T.543, Y.544
Ligand excluded by PLIPSO4.43: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.44: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.7, SO4.81
Ligand excluded by PLIPSO4.47: 2 residues within 4Å:- Chain E: I.26, R.27
Ligand excluded by PLIPSO4.48: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.49: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.63: 3 residues within 4Å:- Chain F: D.34, T.36, Y.38
Ligand excluded by PLIPSO4.64: 3 residues within 4Å:- Chain F: S.204, I.205, A.206
Ligand excluded by PLIPSO4.65: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.66: 4 residues within 4Å:- Chain F: Y.93, H.422, E.423, G.430
Ligand excluded by PLIPSO4.67: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
Ligand excluded by PLIPSO4.68: 12 residues within 4Å:- Chain F: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367
- Ligands: EDO.54, AG.57, AG.58
Ligand excluded by PLIPSO4.69: 2 residues within 4Å:- Chain F: T.470
- Chain I: H.324
Ligand excluded by PLIPSO4.70: 3 residues within 4Å:- Chain F: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.71: 4 residues within 4Å:- Chain F: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.72: 3 residues within 4Å:- Chain F: M.106, D.107, G.108
Ligand excluded by PLIPSO4.73: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.36, SO4.110
Ligand excluded by PLIPSO4.74: 4 residues within 4Å:- Chain F: E.343, E.542, T.543, Y.544
Ligand excluded by PLIPSO4.80: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.81: 8 residues within 4Å:- Chain A: L.15, E.18
- Chain D: L.15, E.18
- Chain G: L.15, E.18
- Ligands: SO4.7, SO4.44
Ligand excluded by PLIPSO4.84: 2 residues within 4Å:- Chain H: I.26, R.27
Ligand excluded by PLIPSO4.85: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.86: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.100: 3 residues within 4Å:- Chain I: D.34, T.36, Y.38
Ligand excluded by PLIPSO4.101: 3 residues within 4Å:- Chain I: S.204, I.205, A.206
Ligand excluded by PLIPSO4.102: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.103: 4 residues within 4Å:- Chain I: Y.93, H.422, E.423, G.430
Ligand excluded by PLIPSO4.104: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
Ligand excluded by PLIPSO4.105: 12 residues within 4Å:- Chain I: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367
- Ligands: EDO.91, AG.94, AG.95
Ligand excluded by PLIPSO4.106: 2 residues within 4Å:- Chain C: H.324
- Chain I: T.470
Ligand excluded by PLIPSO4.107: 3 residues within 4Å:- Chain I: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.108: 4 residues within 4Å:- Chain I: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.109: 3 residues within 4Å:- Chain I: M.106, D.107, G.108
Ligand excluded by PLIPSO4.110: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.36, SO4.73
Ligand excluded by PLIPSO4.111: 4 residues within 4Å:- Chain I: E.343, E.542, T.543, Y.544
Ligand excluded by PLIP- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.13: 7 residues within 4Å:- Chain C: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.14, O.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.8, O.16
NI.14: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.13, O.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.8, O.16
NI.50: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.51, O.53
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.32, O.53
NI.51: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.50, O.53
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.32, O.53
NI.87: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.88, O.90
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.56, O.90
NI.88: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.87, O.90
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.56, O.90
- 3 x O: OXYGEN ATOM(Non-covalent)
O.16: 8 residues within 4Å:- Chain C: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.13, NI.14
No protein-ligand interaction detected (PLIP)O.53: 8 residues within 4Å:- Chain F: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.50, NI.51
No protein-ligand interaction detected (PLIP)O.90: 8 residues within 4Å:- Chain I: H.137, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.87, NI.88
No protein-ligand interaction detected (PLIP)- 6 x AG: SILVER ION(Non-covalent)
AG.20: 5 residues within 4Å:- Chain C: C.322, R.339, M.367
- Ligands: AG.21, SO4.31
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:C.322, H2O.19
AG.21: 5 residues within 4Å:- Chain C: C.322, H.323
- Ligands: EDO.17, AG.20, SO4.31
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:C.322, C:H.323
AG.57: 5 residues within 4Å:- Chain F: C.322, R.339, M.367
- Ligands: AG.58, SO4.68
2 PLIP interactions:1 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:C.322, H2O.43
AG.58: 5 residues within 4Å:- Chain F: C.322, H.323
- Ligands: EDO.54, AG.57, SO4.68
2 PLIP interactions:2 interactions with chain F- Metal complexes: F:C.322, F:H.323
AG.94: 5 residues within 4Å:- Chain I: C.322, R.339, M.367
- Ligands: AG.95, SO4.105
2 PLIP interactions:1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: I:C.322, H2O.67
AG.95: 5 residues within 4Å:- Chain I: C.322, H.323
- Ligands: EDO.91, AG.94, SO4.105
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 1.72 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 45 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 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