3PFV

Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide

Structural Biology Knowledgebase: 3PFV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PFV

Classification: LIGASE / PROTEIN BINDING

Total Structure Weight: 77583.76

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase CBL-B A, B 315 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: N-terminal TKB domain (UNP residues 38-344)
Gene Name(s): CBLB Gene View RNF56 Nbla00127
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
11-meric peptide from Epidermal growth factor receptor C, D 11 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: UNP residues 1066-1076
Gene Name(s): EGFR Gene View ERBB ERBB1 HER1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PG4
Query on PG4

B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
C, D L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.216
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.06 α = 90.00
b = 98.93 β = 110.63
c = 61.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-29
  • Released Date: 2010-12-08
  • Deposition author(s): Chaikuad, A., Guo, K., Cooper, C.D.O., Ayinampudi, V., Krojer, T., Muniz, J.R.C., Vollmar, M., Canning, P., Gileadi, O., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History

  • 2014-04-02
    Type: Source and taxonomy | Details: Corrected source information
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4