8R5C

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

• PDB DOI: https://doi.org/10.2210/pdb8R5C/pdb

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


• Deposited: 2023-11-16 Released: 2024-01-17 
• Deposition Author(s): Munoz Sosa, C.J., Kraemer, A., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

Literature

Crystal structure of human TRIM7 PRYSPRY domain

Munoz Sosa, C.J., Kraemer, A., Knapp, S., Structural Genomics Consortium (SGC)

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: 20.64 kDa 
• Atom Count: 1,595 
• Modelled Residue Count: 172 
• 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
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
Y3C (Subject of Investigation/LOI)	B [auth A]	(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]pentanoic acid C22 H23 N3 O5 HSTLLKBRGCBKBS-ROUUACIJSA-N
SRT	F [auth A], G [auth A]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.716	α = 90
b = 44.594	β = 108.79
c = 59.657	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Munoz Sosa, C.J., Kraemer, A., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

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