3UBP

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE

Structural Biology Knowledgebase: 3UBP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.158

Literature

Macromolecules
Sequence Display for 3UBP

Classification: HYDROLASE

Total Structure Weight: 87023.55

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (UREASE GAMMA SUBUNIT) A 101 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (UREASE BETA SUBUNIT) B 126 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (UREASE ALPHA SUBUNIT) C 570 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Mutation: R19E, G29I, Y36T, Y37T, L38Y, V263L, M420I
Gene Name(s): ureC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2PA
Query on 2PA

C DIAMIDOPHOSPHATE
H5 N2 O2 P
ANCLJVISBRWUTR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

C NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A NON-POLYMER C2 H4 O --
KCX
Query on KCX
C L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.158
  • Space Group: P 63 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.53 α = 90.00
b = 131.53 β = 90.00
c = 188.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-16
  • Released Date: 1999-12-17
  • Deposition author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Miletti, S., Mangani, S., Ciurli, S.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Secondary structure | Details: Secondary structure
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4