1YHS

Crystal structure of Pim-1 bound to staurosporine

Structural Biology Knowledgebase: 1YHS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YHS

Classification: TRANSFERASE

Total Structure Weight: 32140.74

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase Pim-1 A 273 Homo sapiens EC#: 2.7.11.1 IUBMB
Mutation: C161X, S261X
Gene Name(s): PIM1 Gene View

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
STU
Query on STU

A STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
STU IC50: 2.7 - 110 nM (100) BindingDB
Kd: 1.4 - 15 nM (100) BindingDB
ΔG: -48.1 kJ/mol (100) BindingDB
-TΔS: -14 kJ/mol (100) BindingDB

IC50: 10 nM  BindingMOAD
IC50: 10 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.205
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.73 α = 90.00
b = 97.73 β = 90.00
c = 80.51 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-10
  • Released Date: 2005-01-25
  • Deposition author(s): Jacobs, M.D., Black, J., Futer, O., Swenson, L., Hare, B., Fleming, M., Saxena, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4