6LCB | pdb_00006lcb

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009

• PDB DOI: https://doi.org/10.2210/pdb6LCB/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-11-18 Released: 2020-11-25 
• Deposition Author(s): Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009

Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.33 kDa 
• Atom Count: 774 
• Modeled Residue Count: 82 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-1	A	102	Homo sapiens	Mutation(s): 2  Gene Names: DVL1
UniProt & NIH Common Fund Data Resources
Find proteins for O14640 (Homo sapiens) Explore O14640  Go to UniProtKB:  O14640
PHAROS:  O14640 GTEx:  ENSG00000107404

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E83 (Subject of Investigation/LOI)	B [auth A]	2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid C23 H19 N3 O6 S SOWABNTWBBBOPH-NJNXFGOHSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.375	α = 90
b = 85.375	β = 90
c = 46.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description