8HU2

Rattus Syntenin-1 PDZ domain with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8HU2/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-22 Released: 2024-01-17 
• Deposition Author(s): Heo, Y., Lee, J., Yun, J.H., Lee, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Crystal structure of STNPDZ with inhibitor at 1.60 Angstroms resolution.

Heo, Y., Lee, J., Yun, J.H., Lee, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.94 kDa 
• Atom Count: 1,431 
• Modelled Residue Count: 162 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A	163	Rattus norvegicus	Mutation(s): 0  Gene Names: Sdcbp
UniProt
Find proteins for Q9JI92 (Rattus norvegicus) Explore Q9JI92  Go to UniProtKB:  Q9JI92

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M8R (Subject of Investigation/LOI)	B [auth A]	(2~{S})-2-(9~{H}-fluoren-9-ylmethoxycarbonylamino)-3-(4-oxidanylidene-5~{H}-pyrimidin-2-yl)propanoic acid C22 H19 N3 O5 SRYLOGZQEQKDOT-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.098	α = 90
b = 71.098	β = 90
c = 73.072	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Heo, Y., Lee, J., Yun, J.H., Lee, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release