9CPL | pdb_00009cpl

The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker

PDB DOI: https://doi.org/10.2210/pdb9CPL/pdb

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

Deposited: 2024-07-18 Released: 2024-08-14
Deposition Author(s): Samarawickrama, P., Averett, J., 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: 2.40 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.229 (Depositor), 0.220 (DCC)
R-Value Observed:
0.231 (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

1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons

Samarawickrama, P., Ludlow, K., Probst, R., Abiodun, W., Averett, J., Hansen, D., Doukov, T., Moody, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 29.14 kDa
Atom Count: 1,808
Modeled Residue Count: 234
Deposited Residue Count: 251
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein	A	251	Homo sapiens	Mutation(s): 5 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT (Subject of Investigation/LOI) Query on FMT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.229 (Depositor), 0.220 (DCC)
R-Value Observed: 0.231 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39CPL

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.725	α = 90
b = 105.725	β = 90
c = 50.917	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Samarawickrama, P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM146209-01

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.