5HKX | pdb_00005hkx

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

• PDB DOI: https://doi.org/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.214 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.38 kDa 
• Atom Count: 3,219 
• Modeled Residue Count: 374 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

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)
UniProt & NIH Common Fund Data Resources
Find proteins for P22681 (Homo sapiens) Explore P22681  Go to UniProtKB:  P22681
PHAROS:  P22681 GTEx:  ENSG00000110395

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.214 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Zhang, N., Cooper, A., Gao, P., Perez, R.P.

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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
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description