6O02 | pdb_00006o02

Monobody (MC3) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL

PDB DOI: https://doi.org/10.2210/pdb6O02/pdb

Classification: transferase/protein binding
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-02-15 Released: 2020-08-19
Deposition Author(s): Kukenshoner, T., Pojer, F., Hantschel, O.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.217 (Depositor), 0.216 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6O02

This is version 1.1 of the entry. See complete history.

Literature

Monobody (MC3) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL

Kukenshoner, T., Pojer, F., Hantschel, O.

To be published.

Macromolecule Content

Total Structure Weight: 46.3 kDa
Atom Count: 3,232
Modeled Residue Count: 400
Deposited Residue Count: 406
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL	A	309	Homo sapiens	Mutation(s): 0 Gene Names: CBL, CBL2, RNF55 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P22681 (Homo sapiens) Explore P22681 Go to UniProtKB: P22681
PHAROS: P22681 GTEx: ENSG00000110395
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22681
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody (MC3)	B	97	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.217 (Depositor), 0.216 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.356	α = 90
b = 128.356	β = 90
c = 49.007	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-19

Deposition Author(s):

Kukenshoner, T.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	ERC-2016-CoG 682311-ONCOINTRABODY

Revision History (Full details and data files)

Version 1.0: 2020-08-19
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.