- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.87 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 57 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 3 residues within 4Å:- Chain A: K.8
- Ligands: SO4.35, SO4.67
Ligand excluded by PLIPSO4.4: 7 residues within 4Å:- Chain A: A.6, K.10, A.84, T.85, T.90
- Chain C: S.465
- Chain F: F.570
Ligand excluded by PLIPSO4.5: 5 residues within 4Å:- Chain A: F.42, E.59, H.62, V.63
- Ligands: EDO.2
Ligand excluded by PLIPSO4.6: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.8: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.9: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.20: 7 residues within 4Å:- Chain B: P.66, T.69
- Chain C: I.3, Q.7, S.11, Y.12
- Ligands: EDO.12
Ligand excluded by PLIPSO4.21: 4 residues within 4Å:- Chain C: V.16, D.34, T.36, Y.38
Ligand excluded by PLIPSO4.22: 4 residues within 4Å:- Chain C: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.23: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.24: 1 residues within 4Å:- Chain C: Q.501
Ligand excluded by PLIPSO4.25: 2 residues within 4Å:- Chain C: R.513, I.514
Ligand excluded by PLIPSO4.26: 5 residues within 4Å:- Chain C: H.323, K.326, Q.327, N.328, I.329
Ligand excluded by PLIPSO4.27: 2 residues within 4Å:- Chain C: V.16, G.17
Ligand excluded by PLIPSO4.28: 3 residues within 4Å:- Chain C: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.29: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.30: 2 residues within 4Å:- Ligands: SO4.62, SO4.94
Ligand excluded by PLIPSO4.31: 5 residues within 4Å:- Chain C: V.321, L.325
- Chain G: Q.81
- Chain I: T.470
- Ligands: AUF.17
Ligand excluded by PLIPSO4.32: 7 residues within 4Å:- Chain C: A.170, H.222, D.224, H.249, G.280
- Ligands: AUF.17, AUF.18
Ligand excluded by PLIPSO4.35: 3 residues within 4Å:- Chain D: K.8
- Ligands: SO4.3, SO4.67
Ligand excluded by PLIPSO4.36: 7 residues within 4Å:- Chain D: A.6, K.10, A.84, T.85, T.90
- Chain F: S.465
- Chain I: F.570
Ligand excluded by PLIPSO4.37: 5 residues within 4Å:- Chain D: F.42, E.59, H.62, V.63
- Ligands: EDO.34
Ligand excluded by PLIPSO4.38: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.40: 3 residues within 4Å:- Chain E: T.25, I.26, R.27
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.52: 7 residues within 4Å:- Chain E: P.66, T.69
- Chain F: I.3, Q.7, S.11, Y.12
- Ligands: EDO.44
Ligand excluded by PLIPSO4.53: 4 residues within 4Å:- Chain F: V.16, D.34, T.36, Y.38
Ligand excluded by PLIPSO4.54: 4 residues within 4Å:- Chain F: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.55: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.56: 1 residues within 4Å:- Chain F: Q.501
Ligand excluded by PLIPSO4.57: 2 residues within 4Å:- Chain F: R.513, I.514
Ligand excluded by PLIPSO4.58: 5 residues within 4Å:- Chain F: H.323, K.326, Q.327, N.328, I.329
Ligand excluded by PLIPSO4.59: 2 residues within 4Å:- Chain F: V.16, G.17
Ligand excluded by PLIPSO4.60: 3 residues within 4Å:- Chain F: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.61: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.62: 2 residues within 4Å:- Ligands: SO4.30, SO4.94
Ligand excluded by PLIPSO4.63: 5 residues within 4Å:- Chain A: Q.81
- Chain C: T.470
- Chain F: V.321, L.325
- Ligands: AUF.49
Ligand excluded by PLIPSO4.64: 7 residues within 4Å:- Chain F: A.170, H.222, D.224, H.249, G.280
- Ligands: AUF.49, AUF.50
Ligand excluded by PLIPSO4.67: 3 residues within 4Å:- Chain G: K.8
- Ligands: SO4.3, SO4.35
Ligand excluded by PLIPSO4.68: 7 residues within 4Å:- Chain C: F.570
- Chain G: A.6, K.10, A.84, T.85, T.90
- Chain I: S.465
Ligand excluded by PLIPSO4.69: 5 residues within 4Å:- Chain G: F.42, E.59, H.62, V.63
- Ligands: EDO.66
Ligand excluded by PLIPSO4.70: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.72: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.73: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.84: 7 residues within 4Å:- Chain H: P.66, T.69
- Chain I: I.3, Q.7, S.11, Y.12
- Ligands: EDO.76
Ligand excluded by PLIPSO4.85: 4 residues within 4Å:- Chain I: V.16, D.34, T.36, Y.38
Ligand excluded by PLIPSO4.86: 4 residues within 4Å:- Chain I: Y.35, Y.83, I.97, E.429
Ligand excluded by PLIPSO4.87: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.88: 1 residues within 4Å:- Chain I: Q.501
Ligand excluded by PLIPSO4.89: 2 residues within 4Å:- Chain I: R.513, I.514
Ligand excluded by PLIPSO4.90: 5 residues within 4Å:- Chain I: H.323, K.326, Q.327, N.328, I.329
Ligand excluded by PLIPSO4.91: 2 residues within 4Å:- Chain I: V.16, G.17
Ligand excluded by PLIPSO4.92: 3 residues within 4Å:- Chain I: K.33, D.34, Y.35
Ligand excluded by PLIPSO4.93: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.94: 2 residues within 4Å:- Ligands: SO4.30, SO4.62
Ligand excluded by PLIPSO4.95: 5 residues within 4Å:- Chain D: Q.81
- Chain F: T.470
- Chain I: V.321, L.325
- Ligands: AUF.81
Ligand excluded by PLIPSO4.96: 7 residues within 4Å:- Chain I: A.170, H.222, D.224, H.249, G.280
- Ligands: AUF.81, AUF.82
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.13
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, O.13
NI.11: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.10, O.13
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, O.13
NI.42: 8 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.43, O.45
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, O.45
NI.43: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.42, O.45
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, O.45
NI.74: 8 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.75, O.77
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.42, O.77
NI.75: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.74, O.77
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.42, O.77
- 3 x O: OXYGEN ATOM(Non-covalent)
O.13: 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.45: 7 residues within 4Å:- Chain F: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.42, NI.43
No protein-ligand interaction detected (PLIP)O.77: 7 residues within 4Å:- Chain I: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.74, NI.75
No protein-ligand interaction detected (PLIP)- 9 x AUF: triethylphosphanuidylgold(1+)(Non-covalent)
AUF.17: 11 residues within 4Å:- Chain C: K.169, A.170, M.318, V.321, C.322, L.325, A.366
- Chain I: I.468
- Ligands: AUF.18, SO4.31, SO4.32
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:A.170, C:V.321, C:L.325, C:A.366
- Metal complexes: C:C.322
AUF.18: 11 residues within 4Å:- Chain C: A.279, G.280, G.281, M.318, L.319, C.322, I.329, R.339, M.367
- Ligands: AUF.17, SO4.32
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.329, C:R.339
- Metal complexes: C:C.322
AUF.19: 4 residues within 4Å:- Chain C: Q.387, T.554, C.555, E.556
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:E.556
- Metal complexes: C:C.555
AUF.49: 11 residues within 4Å:- Chain C: I.468
- Chain F: K.169, A.170, M.318, V.321, C.322, L.325, A.366
- Ligands: AUF.50, SO4.63, SO4.64
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:A.170, F:V.321, F:L.325, F:A.366
- Metal complexes: F:C.322
AUF.50: 11 residues within 4Å:- Chain F: A.279, G.280, G.281, M.318, L.319, C.322, I.329, R.339, M.367
- Ligands: AUF.49, SO4.64
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:I.329, F:R.339
- Metal complexes: F:C.322
AUF.51: 4 residues within 4Å:- Chain F: Q.387, T.554, C.555, E.556
2 PLIP interactions:2 interactions with chain F- Hydrophobic interactions: F:E.556
- Metal complexes: F:C.555
AUF.81: 11 residues within 4Å:- Chain F: I.468
- Chain I: K.169, A.170, M.318, V.321, C.322, L.325, A.366
- Ligands: AUF.82, SO4.95, SO4.96
5 PLIP interactions:5 interactions with chain I- Hydrophobic interactions: I:A.170, I:V.321, I:L.325, I:A.366
- Metal complexes: I:C.322
AUF.82: 11 residues within 4Å:- Chain I: A.279, G.280, G.281, M.318, L.319, C.322, I.329, R.339, M.367
- Ligands: AUF.81, SO4.96
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:I.329, I:R.339
- Metal complexes: I:C.322
AUF.83: 4 residues within 4Å:- Chain I: Q.387, T.554, C.555, E.556
2 PLIP interactions:2 interactions with chain I- Hydrophobic interactions: I:E.556
- Metal complexes: I:C.555
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition. Dalton Trans (2021)
- Release Date
- 2022-06-01
- 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 1.87 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 57 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x O: OXYGEN ATOM(Non-covalent)
- 9 x AUF: triethylphosphanuidylgold(1+)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition. Dalton Trans (2021)
- Release Date
- 2022-06-01
- 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