SMTL ID : 1s3t.1

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-oligomer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.2, BO3.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.249, C:H.275, H2O.5 NI.2: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.1, BO3.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.137, C:H.139, C:D.363, H2O.5 NI.5: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.6, BO3.8 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.249, F:H.275, H2O.21 NI.6: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.5, BO3.8 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.137, F:H.139, F:D.363, H2O.21 NI.9: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.10, BO3.12 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.249, I:H.275, H2O.37 NI.10: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.9, BO3.12 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.137, I:H.139, I:D.363, H2O.37

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 10 residues within 4Å: Chain C: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339, M.367 Ligands: BO3.4 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.170, C:E.223 Water bridges: C:R.339 Salt bridges: C:H.222, C:H.249, C:H.323, C:R.339 SO4.7: 10 residues within 4Å: Chain F: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339, M.367 Ligands: BO3.8 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:A.170, F:E.223 Water bridges: F:R.339 Salt bridges: F:H.222, F:H.249, F:H.323, F:R.339 SO4.11: 10 residues within 4Å: Chain I: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339, M.367 Ligands: BO3.12 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:A.170, I:E.223 Water bridges: I:R.339 Salt bridges: I:H.222, I:H.249, I:H.323, I:R.339

3 x BO3: BORIC ACID(Non-covalent)

BO3.4: 12 residues within 4Å: Chain C: H.139, A.170, K.220, H.222, H.249, G.280, D.363, A.366, M.367 Ligands: NI.1, NI.2, SO4.3 No protein-ligand interaction detected (PLIP) BO3.8: 12 residues within 4Å: Chain F: H.139, A.170, K.220, H.222, H.249, G.280, D.363, A.366, M.367 Ligands: NI.5, NI.6, SO4.7 No protein-ligand interaction detected (PLIP) BO3.12: 12 residues within 4Å: Chain I: H.139, A.170, K.220, H.222, H.249, G.280, D.363, A.366, M.367 Ligands: NI.9, NI.10, SO4.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism. J.Am.Chem.Soc. (2004)

Release Date

2004-04-06

Peptides

Urease gamma subunit: ADG
Urease beta subunit: BEH
Urease alpha subunit: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

Urease gamma subunit

Urease beta subunit

Urease alpha subunit

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