- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 1 residues within 4Å:- Chain B: R.116
2 PLIP interactions:2 interactions with chain B- Water bridges: B:Q.115
- Salt bridges: B:R.116
SO4.16: 2 residues within 4Å:- Chain C: S.204, I.205
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:I.205
- Water bridges: C:S.203, C:A.206
SO4.17: 3 residues within 4Å:- Chain C: V.558, K.559, E.560
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:K.559, C:E.560
- Water bridges: C:P.557
SO4.18: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.36, SO4.54
3 PLIP interactions:1 interactions with chain C, 1 interactions with chain I, 1 interactions with chain F- Salt bridges: C:K.511, I:K.511, F:K.511
SO4.23: 1 residues within 4Å:- Chain E: R.116
2 PLIP interactions:2 interactions with chain E- Water bridges: E:Q.115
- Salt bridges: E:R.116
SO4.34: 2 residues within 4Å:- Chain F: S.204, I.205
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:I.205
- Water bridges: F:S.203, F:A.206
SO4.35: 3 residues within 4Å:- Chain F: V.558, K.559, E.560
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:K.559, F:E.560
- Water bridges: F:P.557
SO4.36: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.18, SO4.54
3 PLIP interactions:1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F- Salt bridges: I:K.511, C:K.511, F:K.511
SO4.41: 1 residues within 4Å:- Chain H: R.116
2 PLIP interactions:2 interactions with chain H- Water bridges: H:Q.115
- Salt bridges: H:R.116
SO4.52: 2 residues within 4Å:- Chain I: S.204, I.205
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:I.205
- Water bridges: I:S.203, I:A.206
SO4.53: 3 residues within 4Å:- Chain I: V.558, K.559, E.560
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:K.559, I:E.560
- Water bridges: I:P.557
SO4.54: 5 residues within 4Å:- Chain C: K.511
- Chain F: K.511
- Chain I: K.511
- Ligands: SO4.18, SO4.36
3 PLIP interactions:1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F- Salt bridges: I:K.511, C:K.511, F:K.511
- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.6: 9 residues within 4Å:- Chain C: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.7, OH.8, FLC.9
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:H.249, C:H.275, OH.8
NI.7: 7 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.6, OH.8, FLC.9
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:H.137, C:H.139, C:D.363, OH.8
NI.24: 9 residues within 4Å:- Chain F: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.25, OH.26, FLC.27
3 PLIP interactions:2 interactions with chain F, 1 Ligand-Ligand interactions- Metal complexes: F:H.249, F:H.275, OH.26
NI.25: 7 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.24, OH.26, FLC.27
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Ligand interactions- Metal complexes: F:H.137, F:H.139, F:D.363, OH.26
NI.42: 9 residues within 4Å:- Chain I: H.137, K.220, H.222, H.249, H.275, G.280
- Ligands: NI.43, OH.44, FLC.45
3 PLIP interactions:2 interactions with chain I, 1 Ligand-Ligand interactions- Metal complexes: I:H.249, I:H.275, OH.44
NI.43: 7 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.42, OH.44, FLC.45
4 PLIP interactions:3 interactions with chain I, 1 Ligand-Ligand interactions- Metal complexes: I:H.137, I:H.139, I:D.363, OH.44
- 3 x OH: HYDROXIDE ION(Non-covalent)
OH.8: 7 residues within 4Å:- Chain C: H.137, K.220, H.275, D.363
- Ligands: NI.6, NI.7, FLC.9
No protein-ligand interaction detected (PLIP)OH.26: 7 residues within 4Å:- Chain F: H.137, K.220, H.275, D.363
- Ligands: NI.24, NI.25, FLC.27
No protein-ligand interaction detected (PLIP)OH.44: 7 residues within 4Å:- Chain I: H.137, K.220, H.275, D.363
- Ligands: NI.42, NI.43, FLC.45
No protein-ligand interaction detected (PLIP)- 3 x FLC: CITRATE ANION(Non-covalent)
FLC.9: 16 residues within 4Å:- Chain C: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367
- Ligands: NI.6, NI.7, OH.8
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:M.367
- Hydrogen bonds: C:A.366
- Water bridges: C:R.339, C:R.339, C:R.339, C:A.366
- Salt bridges: C:H.137, C:H.139, C:H.222, C:H.249, C:H.249, C:H.275, C:H.323, C:R.339
FLC.27: 16 residues within 4Å:- Chain F: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367
- Ligands: NI.24, NI.25, OH.26
14 PLIP interactions:14 interactions with chain F- Hydrophobic interactions: F:M.367
- Hydrogen bonds: F:A.366
- Water bridges: F:R.339, F:R.339, F:R.339, F:A.366
- Salt bridges: F:H.137, F:H.139, F:H.222, F:H.249, F:H.249, F:H.275, F:H.323, F:R.339
FLC.45: 16 residues within 4Å:- Chain I: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367
- Ligands: NI.42, NI.43, OH.44
14 PLIP interactions:14 interactions with chain I- Hydrophobic interactions: I:M.367
- Hydrogen bonds: I:A.366
- Water bridges: I:R.339, I:R.339, I:R.339, I:A.366
- Salt bridges: I:H.137, I:H.139, I:H.222, I:H.249, I:H.249, I:H.275, I:H.323, I:R.339
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Benini, S. et al., The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design. J.Biol.Inorg.Chem. (2013)
- Release Date
- 2013-01-16
- 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 1.50 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x OH: HYDROXIDE ION(Non-covalent)
- 3 x FLC: CITRATE ANION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Benini, S. et al., The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design. J.Biol.Inorg.Chem. (2013)
- Release Date
- 2013-01-16
- 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