4MJP

E. coli sliding clamp in complex with (R)-Vedaprofen

Structural Biology Knowledgebase: 4MJP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 4MJP

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 82203.09

Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase III subunit beta A, B 366 Escherichia coli EC#: 2.7.7.7 IUBMB
Gene Name(s): dnaN b3701 JW3678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
27O
Query on 27O

B (2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid
(R)-Vedaprofen (Synonym)
C19 H22 O2
VZUGVMQFWFVFBX-CYBMUJFWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A, B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
27O N/A in BindingDB
Ki: 131000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.191
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 79.71 α = 90.00
b = 66.95 β = 113.51
c = 81.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-04
  • Released Date: 2013-09-18
  • Deposition author(s): Yin, Z., Oakley, A.J.

Revision History

  • 2014-06-04
    Type: Citation | Details: Citation update