1C9H

CRYSTAL STRUCTURE OF FKBP12.6 IN COMPLEX WITH RAPAMYCIN

• PDB DOI: https://doi.org/10.2210/pdb1C9H/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-08-02 Released: 2000-08-03 
• Deposition Author(s): Deivanayagam, C.C.S., Carson, M., Thotakura, A., Narayana, S.V.L., Chodavarapu, C.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Structure of FKBP12.6 in complex with rapamycin.

Deivanayagam, C.C., Carson, M., Thotakura, A., Narayana, S.V., Chodavarapu, R.S.

(2000) Acta Crystallogr D Biol Crystallogr 56: 266-271

• PubMed: 10713512 
• DOI: https://doi.org/10.1107/s0907444999016571
• Primary Citation of Related Structures:  
  1C9H


• PubMed Abstract: 
  

  FKBP12.6 is a novel isoform of FKBP12, which selectively binds to the cardiac ryanodine receptor (RyR2). The crystal structure of FKBP12.6 in complex with rapamycin has now been determined at 2.0 A resolution. The structures of FKBP12.6 and FKBP12 are nearly identical, except for a displacement observed in the helical region of FKBP12.6 toward the hydrophobic pocket. This displacement was not predicted by homology modeling studies. Analyses of the residues that are likely to confer the RyR2-binding specificity are presented.

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Organizational Affiliation: 

Center for Macromolecular Crystallography, School of Optometry, 250 BHSB, 1918 University Boulevard, Birmingham, AL 35294--0005, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.58 kDa 
• Atom Count: 984 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FKBP12.6	A	107	Homo sapiens	Mutation(s): 0  Gene Names: CDNA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens) Explore P68106  Go to UniProtKB:  P68106
PHAROS:  P68106 GTEx:  ENSG00000119782

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP	B [auth A]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RAP	BindingDB:  1C9H	Kd: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.696	α = 90
b = 49.288	β = 90
c = 51.694	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
ARP	model building
CNS	refinement
O	model building
OOPS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-03 
Deposition Author(s): Deivanayagam, C.C.S., Carson, M., Thotakura, A., Narayana, S.V.L., Chodavarapu, C.S.

Revision History  

• Version 1.0: 2000-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations