› 5ol4

X-ray diffraction
1.28Å resolution

1.28 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPT

Released:
DOI: 10.2210/pdb5ol4/pdb
PDB entry 5ol4 coloured by chain, front view.
PDB entry 5ol4 coloured by chain, side view.
PDB entry 5ol4 coloured by chain, top view.
Source organism: Sporosarcina pasteurii
Primary publication:
Urease Inhibition in the Presence of N-(n-Butyl)thiophosphoric Triamide, a Suicide Substrate: Structure and Kinetics.
Mazzei L, Cianci M, Contaldo U, Musiani F, Ciurli S
Biochemistry 56 5391-5404 (2017)
PMID: 28857549

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-154232 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Urease subunit gamma Chain: A
Molecule details ›
Chain: A
Length: 100 amino acids
Theoretical weight: 11.13 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41022 (Residues: 1-100; Coverage: 100%)
Gene name: ureA
Sequence domains: Urease, gamma subunit
Structure domains: Urease, gamma-like subunit
Urease subunit beta Chain: B
Molecule details ›
Chain: B
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
Structure domains: Urease, beta subunit
Urease subunit alpha Chain: C
Molecule details ›
Chain: C
Length: 570 amino acids
Theoretical weight: 61.58 KDa
Source organism: Sporosarcina pasteurii
UniProt:
  • Canonical: P41020 (Residues: 1-34, 35-570; Coverage: 100%)
Gene names: NCTC4822_02163, ureC
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand EDO 17 x EDO
Ligand SO4 3 x SO4
Ligand NI 2 x NI
Ligand 9XN 1 x 9XN
2 modified residues:
Ligand CXM 1 x CXM
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P6322
Unit cell:
a: 131.742Å b: 131.742Å c: 188.93Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.12 0.119 0.137

Quick links

Citations

1 review citation

Recent advances in design of new urease inhibitors: A review.
Kafarski et al. (2018)
7 other articles

2 mentions without citation

The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate.
Mazzei et al. (2020)
1 more