Macromolecule Content

Total Structure Weight: 45.38 kDa
Atom Count: 3219
Residue Count: 374
Unique protein chains: 1

5HKX

Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution

DOI: 10.2210/pdb5HKX/pdb

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

Deposited: 2016-01-14 Released: 2017-01-18
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Zhang, N., Cooper, A., Gao, P., Perez, R.P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution

Zhang, N., Ferris, D., Lovell, S., Smalter-Hall, A., Battaile, K.P., Anbanandam, A., Gao, P., Hanzlik, R., Perez, R.P.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL	A	392	Homo sapiens	Mutation(s): 1 Gene Names: CBL, CBL2, RNF55 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for P22681 (Homo sapiens) Explore P22681 Go to UniProtKB: P22681
NIH Common Fund Data Resources
PHAROS: P22681 GTEx: ENSG00000110395
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] MOL2 format, chain C [A] MOL2 format, chain D [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [A] MOL2 format, chain E [A]	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.075	α = 90
b = 108.737	β = 115.31
c = 49.304	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2016-01-14
Released Date: 2017-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5P20RR017708-10 / 8P20GM103420-10

Revision History

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-25
Changes: Author supporting evidence

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.