8R5B | pdb_00008r5b

Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-L-glutamine

• PDB DOI: https://doi.org/10.2210/pdb8R5B/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: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-L-glutamine

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

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.3 kDa 
• Atom Count: 3,101 
• Modeled Residue Count: 338 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM7	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y32 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{S})-5-azanyl-5-oxidanylidene-2-[(3-phenoxyphenyl)carbonylamino]pentanoic acid C18 H18 N2 O5 MLMXIRRYCOORCS-HNNXBMFYSA-N
ACY	E [auth B], F [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.189	α = 90
b = 87.436	β = 90
c = 122.242	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