Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.82 kDa 
• Atom Count: 2071 
• Modelled Residue Count: 210 
• Deposited Residue Count: 216 
• Unique protein chains: 1

5IXB

Structure of human Melanoma Inhibitory Activity (MIA) Protein in complex with Pyrimidin-2-amine

• PDB DOI: 10.2210/pdb5IXB/pdb

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


• Deposited: 2016-03-23 Released: 2016-08-17 
• Deposition Author(s): Yip, K.T., Gasper, R., Zhong, X.Y., Seibel, N., Puetz, S., Autzen, J., Scherkenbeck, J., Hofmann, E., Stoll, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.160 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 

Literature

Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma.

Yip, K.T., Zhong, X.Y., Seibel, N., Putz, S., Autzen, J., Gasper, R., Hofmann, E., Scherkenbeck, J., Stoll, R.

(2016) Sci Rep 6: 25119-25119

• PubMed: 27151361 
• DOI: 10.1038/srep25119
• Primary Citation of Related Structures:  
  5IXB


• PubMed Abstract: 
  

Melanoma inhibitory activity (MIA), an extracellular protein highly expressed by malignant melanoma cells, plays an important functional role in melanoma development, progression, and metastasis. After its secretion, MIA directly interacts with extracellular matrix proteins, such as fibronectin (FN). By this mechanism, MIA actively facilitates focal cell detachment from surrounding structures and strongly promotes tumour cell invasion and migration. Hence, the molecular understanding of MIA's function provides a promising target for the development of new strategies in malignant melanoma therapy. Here, we describe for the first time the discovery of small molecules that are able to disrupt the MIA-FN complex by selectively binding to a new druggable pocket, which we could identify on MIA by structural analysis and fragment-based screening. Our findings may inspire novel drug discovery efforts aiming at a therapeutically effective treatment of melanoma by targeting MIA.

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Organizational Affiliation: 

Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma-derived growth regulatory protein	A, B	108	Homo sapiens	Mutation(s): 0  Gene Names: MIA
UniProt & NIH Common Fund Data Resources
Find proteins for Q16674 (Homo sapiens) Explore Q16674  Go to UniProtKB:  Q16674
PHAROS:  Q16674

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGA	C [auth A], E [auth B]	PYRIMIDIN-2-AMINE C4 H5 N3 LJXQPZWIHJMPQQ-UHFFFAOYSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.160 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.44	α = 90
b = 47.48	β = 90
c = 87.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-23 
• Released Date: 2016-08-17 
Deposition Author(s): Yip, K.T., Gasper, R., Zhong, X.Y., Seibel, N., Puetz, S., Autzen, J., Scherkenbeck, J., Hofmann, E., Stoll, R.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release