4E6W

ClbP in complex with 3-aminophenyl boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The NRP peptidase ClbP as a target for the inhibition of genotoxicity, cell proliferation and tumorogenesis mediated by pks-harboring bacteria

Cougnoux, A.Delmas, J.Dalmasso, G.Romagnoli, C.Cuevas-Ramos, G.Oswald, E.Parti, F.Bonnet, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ClbP peptidase
A, B, C
335Escherichia coli O6Mutation(s): 0 
Gene Names: c2452
EC: 3.5.2.6
UniProt
Find proteins for A0A0H2V8D3 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore A0A0H2V8D3 
Go to UniProtKB:  A0A0H2V8D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2V8D3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APB
Query on APB

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
M-AMINOPHENYLBORONIC ACID
C6 H8 B N O2
JMZFEHDNIAQMNB-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.49α = 90
b = 149.36β = 124.21
c = 88.24γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary