8HCK

NMR fragment-based screening against the two PDZ do-mains of MDA-9

• PDB DOI: https://doi.org/10.2210/pdb8HCK/pdb

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


• Deposited: 2022-11-01 Released: 2023-11-08 
• Deposition Author(s): Tang, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 
• R-Value Observed: 0.237 

Literature

NMR fragment-based screening against the two PDZ do-mains of MDA-9

Tang, H.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 9.64 kDa 
• Atom Count: 675 
• Modelled Residue Count: 81 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A	81	Homo sapiens	Mutation(s): 0  Gene Names: SDCBP, MDA9, SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens) Explore O00560  Go to UniProtKB:  O00560
PHAROS:  O00560 GTEx:  ENSG00000137575

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P1Z (Subject of Investigation/LOI)	B [auth A]	4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE C19 H20 N2 O2 VYMDGNCVAMGZFE-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 
• R-Value Observed: 0.237 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.353	α = 90
b = 49.353	β = 90
c = 75.254	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Tang, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary