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

• PDB DOI: https://doi.org/10.2210/pdb3B76/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-30 Released: 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Starting Models: experimental

Literature

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.

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.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.8 kDa 
• Atom Count: 1,654 
• Modelled Residue Count: 203 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase LNX	A, B	118	Homo sapiens	Mutation(s): 0  Gene Names: LNX1, LNX EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBB1 (Homo sapiens) Explore Q8TBB1  Go to UniProtKB:  Q8TBB1
GTEx:  ENSG00000072201

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth B], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.782	α = 90
b = 58.449	β = 90
c = 73.741	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description