7HNH | pdb_00007hnh

PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z2643472210

• PDB DOI: https://doi.org/10.2210/pdb7HNH/pdb
• Deposition Group: G_1002320 (changed state) | Explore  G_1002320  

• Classification: LIGASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-04 Released: 2024-11-27 
• Deposition Author(s): Kim, Y., Marples, P., Fearon, D., von Delft, F., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Kim, Y., Marples, P., Fearon, D., von Delft, F., 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.

Macromolecule Content 

• Total Structure Weight: 22.26 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 185 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A [auth B]	188	Mus musculus	Mutation(s): 0  Gene Names: Trim21, Ro52, Ssa1 EC: 2.3.2.27
UniProt
Find proteins for Q62191 (Mus musculus) Explore Q62191  Go to UniProtKB:  Q62191

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
A1BFW (Subject of Investigation/LOI)	C [auth B]	1-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1H-pyrazole-3-carboxamide C10 H15 N3 O2 WBAZBPMBDLSPCX-UHFFFAOYSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B, E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.555	α = 90
b = 95.555	β = 90
c = 45.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Kim, Y., Marples, P., Fearon, D., von Delft, F., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	875510

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release