1PKG

Structure of a c-Kit Kinase Product Complex

Structural Biology Knowledgebase: 1PKG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 1PKG

Classification: TRANSFERASE ACTIVATOR

Total Structure Weight: 76009.99

Macromolecule Entities
Molecule Chains Length Organism Details
c-kit protein A, B 329 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: catalytic domain
Mutation: Y568X, Y570X
Gene Name(s): KIT Gene View SCFR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.225
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 92.67 α = 90.00
b = 116.46 β = 90.00
c = 60.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-05
  • Released Date: 2003-08-12
  • Deposition author(s): Mol, C.D., Lim, K.B., Sridhar, V., Zou, H., Chien, E.Y.T., Sang, B.-C., Nowakowski, J., Kassel, D.B., Cronin, C.N., McRee, D.E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values