- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.42 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 33 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 1 residues within 4Å:- Chain B: R.112
3 PLIP interactions:3 interactions with chain B- Water bridges: B:R.112, B:R.112
- Salt bridges: B:R.112
SO4.15: 8 residues within 4Å:- Chain C: K.326, I.329
- Chain H: S.67, G.68
- Chain I: S.11, Y.12, N.43, K.48
7 PLIP interactions:2 interactions with chain C, 4 interactions with chain I, 1 interactions with chain H- Water bridges: C:K.326, I:N.43, I:N.43
- Salt bridges: C:K.326, I:K.48
- Hydrogen bonds: I:S.11, H:G.68
SO4.23: 1 residues within 4Å:- Chain E: R.112
3 PLIP interactions:3 interactions with chain E- Water bridges: E:R.112, E:R.112
- Salt bridges: E:R.112
SO4.32: 8 residues within 4Å:- Chain B: S.67, G.68
- Chain C: S.11, Y.12, N.43, K.48
- Chain F: K.326, I.329
7 PLIP interactions:4 interactions with chain C, 1 interactions with chain B, 2 interactions with chain F- Hydrogen bonds: C:S.11, B:G.68
- Water bridges: C:N.43, C:N.43, F:K.326
- Salt bridges: C:K.48, F:K.326
SO4.40: 1 residues within 4Å:- Chain H: R.112
3 PLIP interactions:3 interactions with chain H- Water bridges: H:R.112, H:R.112
- Salt bridges: H:R.112
SO4.49: 8 residues within 4Å:- Chain E: S.67, G.68
- Chain F: S.11, Y.12, N.43, K.48
- Chain I: K.326, I.329
7 PLIP interactions:4 interactions with chain F, 2 interactions with chain I, 1 interactions with chain E- Hydrogen bonds: F:S.11, E:G.68
- Water bridges: F:N.43, F:N.43, I:K.326
- Salt bridges: F:K.48, I:K.326
- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.7: 8 residues within 4Å:- Chain C: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.8, F.16, URE.17
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:H.249, C:H.275, URE.17
NI.8: 7 residues within 4Å:- Chain C: H.137, H.139, K.220, D.363
- Ligands: NI.7, F.16, URE.17
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:H.137, C:H.139, C:D.363
NI.24: 8 residues within 4Å:- Chain F: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.25, F.33, URE.34
3 PLIP interactions:2 interactions with chain F, 1 Ligand-Ligand interactions- Metal complexes: F:H.249, F:H.275, URE.34
NI.25: 7 residues within 4Å:- Chain F: H.137, H.139, K.220, D.363
- Ligands: NI.24, F.33, URE.34
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:H.137, F:H.139, F:D.363
NI.41: 8 residues within 4Å:- Chain I: K.220, H.222, H.249, H.275, G.280
- Ligands: NI.42, F.50, URE.51
2 PLIP interactions:2 interactions with chain I- Metal complexes: I:H.249, I:H.275
NI.42: 7 residues within 4Å:- Chain I: H.137, H.139, K.220, D.363
- Ligands: NI.41, F.50, URE.51
3 PLIP interactions:3 interactions with chain I- Metal complexes: I:H.137, I:H.139, I:D.363
- 3 x F: FLUORIDE ION(Non-covalent)
F.16: 8 residues within 4Å:- Chain C: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.7, NI.8, URE.17
No protein-ligand interaction detected (PLIP)F.33: 8 residues within 4Å:- Chain F: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.24, NI.25, URE.34
No protein-ligand interaction detected (PLIP)F.50: 8 residues within 4Å:- Chain I: H.137, K.220, H.275, G.280, D.363
- Ligands: NI.41, NI.42, URE.51
No protein-ligand interaction detected (PLIP)- 3 x URE: UREA(Non-functional Binders)
URE.17: 15 residues within 4Å:- Chain C: H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, D.363, A.366, M.367
- Ligands: NI.7, NI.8, F.16
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:A.366
URE.34: 15 residues within 4Å:- Chain F: H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, D.363, A.366, M.367
- Ligands: NI.24, NI.25, F.33
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:A.366
URE.51: 15 residues within 4Å:- Chain I: H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, D.363, A.366, M.367
- Ligands: NI.41, NI.42, F.50
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:H.249, I:A.366, I:A.366
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme. Angew.Chem.Int.Ed.Engl. (2019)
- Release Date
- 2019-11-13
- 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 1.42 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 33 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 3 x F: FLUORIDE ION(Non-covalent)
- 3 x URE: UREA(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mazzei, L. et al., The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme. Angew.Chem.Int.Ed.Engl. (2019)
- Release Date
- 2019-11-13
- 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