5HKY | pdb_00005hky

Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8A Resolution (P6 form)

• PDB DOI: https://doi.org/10.2210/pdb5HKY/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: 1.80 Å
• R-Value Free: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8A Resolution (P6 form)

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: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 39.03 kDa 
• Atom Count: 2,943 
• Modeled Residue Count: 325 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL	A	308	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein sprouty homolog 2	B	26	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for O43597 (Homo sapiens) Explore O43597  Go to UniProtKB:  O43597
PHAROS:  O43597 GTEx:  ENSG00000136158

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.81	α = 90
b = 122.81	β = 90
c = 58.44	γ = 120

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, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary