9NGE | pdb_00009nge

The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone

PDB DOI: https://doi.org/10.2210/pdb9NGE/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-02-22 Released: 2025-03-26
Deposition Author(s): Averett, J.C., Bradford, M.J., Averett, B.J., Hansen, D., Doukov, T., Moody, J.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.213 (Depositor), 0.213 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone

Averett, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 39.11 kDa
Atom Count: 2,424
Modeled Residue Count: 305
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1	A, B	165	Homo sapiens	Mutation(s): 6 Gene Names: ETV6, TEL, TEL1, TNK1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens) Explore P41212 Go to UniProtKB: P41212
PHAROS: P41212 GTEx: ENSG00000139083
Find proteins for Q13470 (Homo sapiens) Explore Q13470 Go to UniProtKB: Q13470
PHAROS: Q13470 GTEx: ENSG00000174292
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P41212Q13470
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B]	F [auth A], G [auth A], H [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.213 (Depositor), 0.213 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.935	α = 90
b = 77.487	β = 106.99
c = 38.342	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data scaling
autoPROC	data reduction
PHASER	phasing
PHENIX	refinement
PDB-REDO	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM146209
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM155011