2DG4

FK506-binding protein mutant WF59 complexed with Rapamycin

Structural Biology Knowledgebase: 2DG4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DG4

Classification: ISOMERASE

Total Structure Weight: 12803.85

Macromolecule Entities
Molecule Chains Length Organism Details
FK506-binding protein 1A A 107 Homo sapiens EC#: 5.2.1.8 IUBMB
Mutation: W59F
Gene Name(s): FKBP1A Gene View FKBP1 FKBP12

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

A RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RAP EC50: 30 nM (99) BindingDB
IC50: 0.45 - 1.6 nM (99) BindingDB
Ki: 0.2 - 1 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.195
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 44.49 α = 90.00
b = 49.10 β = 90.00
c = 51.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-08
  • Released Date: 2006-04-25
  • Deposition author(s): Buckle, A.M.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4