4UBP

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION

Structural Biology Knowledgebase: 4UBP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.151

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4UBP

Classification: HYDROLASE

Total Structure Weight: 87002.60

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (UREASE (CHAIN A)) A 101 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureA
PROTEIN (UREASE (CHAIN B)) B 126 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureB
PROTEIN (UREASE (CHAIN C)) C 570 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Mutation: R19E, G28W, Y36T, Y37T, L38Y, K220X, V263L, M420I
Gene Name(s): ureC

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

C ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

C NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HAE N/A in BindingDB
Ki: 2600 nM  BindingMOAD
N/A in PDBbind
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: 1.55 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.151
  • Space Group: P 63 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 130.88 α = 90.00
b = 130.88 β = 90.00
c = 189.00 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-02-25
  • Released Date: 2000-03-06
  • Deposition author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

Revision History

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