1M2Z

Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif

Structural Biology Knowledgebase: 1M2Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 1M2Z

Classification: HORMONE / HORMONE ACTIVATOR

Total Structure Weight: 66183.56

Macromolecule Entities
Molecule Chains Length Organism Details
glucocorticoid receptor A, D 257 Homo sapiens Fragment: Ligand Binding Domain, residues 521-777
Mutation: F602S
Gene Name(s): NR3C1 Gene View GRL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
nuclear receptor coactivator 2 B, E 21 Homo sapiens Fragment: TIF2 coactivator motif, residues 734-754
Gene Name(s): NCOA2 Gene View BHLHE75 SRC2 TIF2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, D DEXAMETHASONE
9A-FLUORO-16BETA-METHYLPREDNISOLONE (Synonym)
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

A B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DEX EC50: 0.2 - 17 nM (99) BindingDB
IC50: 0.5 - 22 nM (95 - 99) BindingDB
Kd: 19 nM (99) BindingDB
Ki: 0.69 - 5.5 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.237
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 125.84 α = 90.00
b = 125.84 β = 90.00
c = 85.98 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-26
  • Released Date: 2003-07-15
  • Deposition author(s): Bledsoe, R.B., Montana, V.G., Stanley, T.B., Delves, C.J., Apolito, C.J., Mckee, D.D., Consler, T.G., Parks, D.J., Stewart, E.L., Willson, T.M., Lambert, M.H., Moore, J.T., Pearce, K.H., Xu, H.E.

Revision History

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