› 6zo3

X-ray diffraction
1.55Å resolution

1.55 A resolution 3,6-dimethylcatechol (3,6-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease

Released:
DOI: 10.2210/pdb6zo3/pdb
Model geometry
Fit model/data
PDB entry 6zo3 coloured by chain, front view.
PDB entry 6zo3 coloured by chain, side view.
PDB entry 6zo3 coloured by chain, top view.
Source organism: Sporosarcina pasteurii
Primary publication:
Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies.
Mazzei L, Contaldo U, Musiani F, Cianci M, Bagnolini G, Roberti M, Ciurli S
Angew Chem Int Ed Engl 60 6029-6035 (2021)
PMID: 33245574

Function and Biology Details

Reaction catalysed: 
Urea + H(2)O = CO(2) + 2 NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
PDBe Complex ID:
PDB-CPX-102189 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Urease subunit gamma Chain: AAA
Molecule details ›
Chain: AAA
Length: 100 amino acids
Theoretical weight: 11.13 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: A0A0H3YGY5 (Residues: 1-100; Coverage: 100%)
Gene names: NCTC4822_02165, ureA
Sequence domains: Urease, gamma subunit
Urease subunit beta Chain: BBB
Molecule details ›
Chain: BBB
Length: 122 amino acids
Theoretical weight: 13.53 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41021 (Residues: 5-126; Coverage: 97%)
Gene name: ureB
Sequence domains: Urease beta subunit
Urease subunit alpha Chain: CCC

Ligands and Environments

4 bound ligands:
Ligand EDO 20 x EDO
Ligand SO4 6 x SO4
Ligand NI 2 x NI
Ligand OH 1 x OH
3 modified residues:
Ligand CXM 1 x CXM
Ligand KCX 1 x KCX
Ligand QNT 1 x QNT

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P6322
Unit cell:
a: 131.463Å b: 131.463Å c: 189.067Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.136 0.136 0.156

Quick links

Citations

5 citation in other articles

A small-molecular inhibitor against Proteus mirabilis urease to treat catheter-associated urinary tract infections.
Milo et al. (2021)
4 more