9HIN | pdb_00009hin

Crystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine

• PDB DOI: https://doi.org/10.2210/pdb9HIN/pdb

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


• Deposited: 2024-11-26 Released: 2025-01-15 
• Deposition Author(s): Lenz, C., Haman, A., Spissinger, H., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine

Lenz, C., Haman, A., Spissinger, H., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

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: 20.48 kDa 
• Atom Count: 1,476 
• Modeled Residue Count: 170 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM7	A	175	Homo sapiens	Mutation(s): 0  Gene Names: TRIM7 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C029 (Homo sapiens) Explore Q9C029  Go to UniProtKB:  Q9C029
PHAROS:  Q9C029 GTEx:  ENSG00000146054

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IU9 (Subject of Investigation/LOI)	C [auth A]	((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine C28 H28 N4 O6 CGCOMGPOOJVYAL-GOTSBHOMSA-N
TLA (Subject of Investigation/LOI)	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.784	α = 90
b = 44.154	β = 107.54
c = 57.343	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Lenz, C., Haman, A., Spissinger, H., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release