- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.68 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 63 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 48 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 2 residues within 4Å:- Chain A: K.29
- Ligands: EDO.3
Ligand excluded by PLIPSO4.8: 3 residues within 4Å:- Chain A: M.70, E.71
- Chain C: R.566
Ligand excluded by PLIPSO4.9: 2 residues within 4Å:- Chain A: N.97
- Chain F: K.326
Ligand excluded by PLIPSO4.10: 6 residues within 4Å:- Chain A: F.14, E.18
- Chain D: L.15, E.18
- Ligands: SO4.51, SO4.92
Ligand excluded by PLIPSO4.14: 3 residues within 4Å:- Chain B: T.25, I.26, R.27
Ligand excluded by PLIPSO4.15: 3 residues within 4Å:- Chain B: G.101, S.102, N.105
Ligand excluded by PLIPSO4.16: 2 residues within 4Å:- Chain B: L.108, R.112
Ligand excluded by PLIPSO4.17: 5 residues within 4Å:- Chain A: E.75
- Chain B: V.4, P.5, G.6, E.7
Ligand excluded by PLIPSO4.18: 6 residues within 4Å:- Chain B: R.27, V.28, S.29, L.52, F.53, E.78
Ligand excluded by PLIPSO4.35: 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 PLIPSO4.36: 6 residues within 4Å:- Chain B: S.67, G.68
- Chain C: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.37: 2 residues within 4Å:- Chain C: S.204, I.205
Ligand excluded by PLIPSO4.38: 4 residues within 4Å:- Chain C: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.39: 1 residues within 4Å:- Chain C: K.518
Ligand excluded by PLIPSO4.40: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.81, SO4.122
Ligand excluded by PLIPSO4.41: 4 residues within 4Å:- Chain C: K.33, D.34, Y.35
- Ligands: EDO.25
Ligand excluded by PLIPSO4.48: 2 residues within 4Å:- Chain D: K.29
- Ligands: EDO.44
Ligand excluded by PLIPSO4.49: 3 residues within 4Å:- Chain D: M.70, E.71
- Chain F: R.566
Ligand excluded by PLIPSO4.50: 2 residues within 4Å:- Chain D: N.97
- Chain I: K.326
Ligand excluded by PLIPSO4.51: 6 residues within 4Å:- Chain D: F.14, E.18
- Chain G: L.15, E.18
- Ligands: SO4.10, SO4.92
Ligand excluded by PLIPSO4.55: 3 residues within 4Å:- Chain E: T.25, I.26, R.27
Ligand excluded by PLIPSO4.56: 3 residues within 4Å:- Chain E: G.101, S.102, N.105
Ligand excluded by PLIPSO4.57: 2 residues within 4Å:- Chain E: L.108, R.112
Ligand excluded by PLIPSO4.58: 5 residues within 4Å:- Chain D: E.75
- Chain E: V.4, P.5, G.6, E.7
Ligand excluded by PLIPSO4.59: 6 residues within 4Å:- Chain E: R.27, V.28, S.29, L.52, F.53, E.78
Ligand excluded by PLIPSO4.76: 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 PLIPSO4.77: 6 residues within 4Å:- Chain E: S.67, G.68
- Chain F: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.78: 2 residues within 4Å:- Chain F: S.204, I.205
Ligand excluded by PLIPSO4.79: 4 residues within 4Å:- Chain F: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.80: 1 residues within 4Å:- Chain F: K.518
Ligand excluded by PLIPSO4.81: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.40, SO4.122
Ligand excluded by PLIPSO4.82: 4 residues within 4Å:- Chain F: K.33, D.34, Y.35
- Ligands: EDO.66
Ligand excluded by PLIPSO4.89: 2 residues within 4Å:- Chain G: K.29
- Ligands: EDO.85
Ligand excluded by PLIPSO4.90: 3 residues within 4Å:- Chain G: M.70, E.71
- Chain I: R.566
Ligand excluded by PLIPSO4.91: 2 residues within 4Å:- Chain C: K.326
- Chain G: N.97
Ligand excluded by PLIPSO4.92: 6 residues within 4Å:- Chain A: L.15, E.18
- Chain G: F.14, E.18
- Ligands: SO4.10, SO4.51
Ligand excluded by PLIPSO4.96: 3 residues within 4Å:- Chain H: T.25, I.26, R.27
Ligand excluded by PLIPSO4.97: 3 residues within 4Å:- Chain H: G.101, S.102, N.105
Ligand excluded by PLIPSO4.98: 2 residues within 4Å:- Chain H: L.108, R.112
Ligand excluded by PLIPSO4.99: 5 residues within 4Å:- Chain G: E.75
- Chain H: V.4, P.5, G.6, E.7
Ligand excluded by PLIPSO4.100: 6 residues within 4Å:- Chain H: R.27, V.28, S.29, L.52, F.53, E.78
Ligand excluded by PLIPSO4.117: 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 PLIPSO4.118: 6 residues within 4Å:- Chain H: S.67, G.68
- Chain I: S.11, Y.12, N.43, K.48
Ligand excluded by PLIPSO4.119: 2 residues within 4Å:- Chain I: S.204, I.205
Ligand excluded by PLIPSO4.120: 4 residues within 4Å:- Chain I: K.386, V.558, K.559, E.560
Ligand excluded by PLIPSO4.121: 1 residues within 4Å:- Chain I: K.518
Ligand excluded by PLIPSO4.122: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.40, SO4.81
Ligand excluded by PLIPSO4.123: 4 residues within 4Å:- Chain I: K.33, D.34, Y.35
- Ligands: EDO.107
Ligand excluded by PLIP- 3 x IS9: dimethylcarbamodithioic acid(Non-covalent)
IS9.31: 5 residues within 4Å:- Chain C: V.321, C.322
- Chain G: Q.81
- Chain I: I.468, T.470
No protein-ligand interaction detected (PLIP)IS9.72: 5 residues within 4Å:- Chain A: Q.81
- Chain C: I.468, T.470
- Chain F: V.321, C.322
No protein-ligand interaction detected (PLIP)IS9.113: 5 residues within 4Å:- Chain D: Q.81
- Chain F: I.468, T.470
- Chain I: V.321, C.322
No protein-ligand interaction detected (PLIP)- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.32: 7 residues within 4Å:- Chain C: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.33, OH.34
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, OH.34
NI.33: 6 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.32, OH.34
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, OH.34
NI.73: 7 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.74, OH.75
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.75
NI.74: 6 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.73, OH.75
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.29, OH.75
NI.114: 7 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.115, OH.116
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.50, OH.116
NI.115: 6 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.114, OH.116
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.50, OH.116
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.34: 9 residues within 4Å:- Chain C: H.137, H.139, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.32, NI.33
No protein-ligand interaction detected (PLIP)OH.75: 9 residues within 4Å:- Chain F: H.137, H.139, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.73, NI.74
No protein-ligand interaction detected (PLIP)OH.116: 9 residues within 4Å:- Chain I: H.137, H.139, K.220, H.249, H.275, G.280, D.363
- Ligands: NI.114, NI.115
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Kinetic and structural details of urease inactivation by thiuram disulphides. J.Inorg.Biochem. (2023)
- Release Date
- 2023-11-01
- 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 1.68 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 63 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 48 x SO4: SULFATE ION(Non-functional Binders)
- 3 x IS9: dimethylcarbamodithioic acid(Non-covalent)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x OH: HYDROXIDE ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., Kinetic and structural details of urease inactivation by thiuram disulphides. J.Inorg.Biochem. (2023)
- Release Date
- 2023-11-01
- 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