3B76

Crystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor

Structural Biology Knowledgebase: 3B76 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.175

Literature

Macromolecules
Sequence Display for 3B76

Classification: LIGASE

Total Structure Weight: 25796.34

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase LNX A, B 118 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: Third PDZ domain: Residues 504-594
Gene Name(s): LNX1 Gene View LNX PDZRN2 UNQ574/PRO1136
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.175
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.78 α = 90.00
b = 58.45 β = 90.00
c = 73.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-10-30
  • Released Date: 2007-11-13
  • Deposition author(s): Ugochukwu, E., Burgess-Brown, N., Berridge, G., Elkins, J., Bunkoczi, G., Pike, A.C.W., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Gileadi, O., von Delft, F., Doyle, D., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor