3UBP Hydrolase date Dec 16, 1998
title Diamidophosphate Inhibited Bacillus Pasteurii Urease
authors S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Mangani, S.Ciu
compound source
Molecule: Protein (Urease Gamma Subunit)
Chain: A
Synonym: Urea Aminohydrolase
Ec: 3.5.1.5
Organism_scientific: Sporosarcina Pasteurii
Organism_taxid: 1474
Strain: Dsm 33
Cellular_location: Cytoplasm

Molecule: Protein (Urease Beta Subunit)
Chain: B
Synonym: Urea Aminohydrolase
Ec: 3.5.1.5

Organism_scientific: Sporosarcina Pasteurii
Organism_taxid: 1474
Strain: Dsm 33
Cellular_location: Cytoplasm

Molecule: Protein (Urease Alpha Subunit)
Chain: C
Synonym: Urea Aminohydrolase
Ec: 3.5.1.5

Organism_scientific: Sporosarcina Pasteurii
Organism_taxid: 1474
Strain: Dsm 33
Cellular_location: Cytoplasm
symmetry Space Group: P 63 2 2
R_factor 0.158 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.532 131.532 188.451 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand 2PA, ACE, KCX, NI enzyme Hydrolase E.C.3.5.1.5 BRENDA
related structures by homologous chain: 1EJW, 1UBP, 2UBP
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


Primary referenceA new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels., Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S, Structure Fold Des 1999 Feb 15;7(2):205-16. PMID:10368287
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (3ubp.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (3ubp.pdb2.gz) 401 Kb
  • LPC: Ligand-Protein Contacts for 3UBP
  • CSU: Contacts of Structural Units for 3UBP
  • Likely Quarternary Molecular Structure file(s) for 3UBP
  • Structure Factors (622 Kb)
  • Retrieve 3UBP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UBP from S2C, [Save to disk]
  • Re-refined 3ubp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UBP in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3UBP
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3UBP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d3ubpa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d3ubpb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d3ubpc1, region C:1-131,C:435-483 [Jmol] [rasmolscript] [script source]
        - Domain d3ubpc2, region C:132-434,C:484-570 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ubp] [3ubp_C] [3ubp_B] [3ubp_A]
  • SWISS-PROT database: [P41020] [P41021] [P41022]
  • Domain organization of [URE1_BACPA] [URE2_BACPA] [URE3_BACPA] by SWISSPFAM
  • Other resources with information on 3UBP
  • Community annotation for 3UBP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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