4DH0

X-ray Crystal Structure of 28-O-Methylrapamycin complexed with FKBP12: Is the Cyclohexyl Moiety Part of the Effector Domain of Rapamycin?

• PDB DOI: https://doi.org/10.2210/pdb4DH0/pdb

• Classification: ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-27 Released: 2012-02-15 
• Deposition Author(s): Kallen, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

X-ray Crystal Structure of 28-O-Methylrapamycin complexed with FKBP12: Is the Cyclohexyl Moiety Part of the Effector Domain of Rapamycin?

Kallen, J., Sedrani, R., Cottens, S.

(1996) J Am Chem Soc 118: 5857-5861

• DOI: https://doi.org/10.1021/ja954328h

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.76 kDa 
• Atom Count: 974 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	107	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1A, FKBP1, FKBP12 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MR8	B [auth A]	28-O-Methylrapamycin C52 H81 N O13 TXZXMCLTSBPVQD-JQEUAWNDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.5	α = 90
b = 49.7	β = 90
c = 55.3	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
X-PLOR	model building
REFMAC	refinement
MADNESS	data reduction
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-04-18
  Changes: Data collection
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations