8PPZ

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR

• PDB DOI: https://doi.org/10.2210/pdb8PPZ/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-07-10 Released: 2023-08-09 
• Deposition Author(s): Meyners, C., Deutscher, R.C.E., Hausch, F.
• Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.238 
• R-Value Work: 0.192 

Starting Model: experimental

Literature

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR

Meyners, C., Deutscher, R.C.E., Hausch, F.

(2023) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2023-4vb0m

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 24.39 kDa 
• Atom Count: 1,766 
• Modelled Residue Count: 201 
• Deposited Residue Count: 205 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	107	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	B	98	Homo sapiens	Mutation(s): 0  Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345  Go to UniProtKB:  P42345
PHAROS:  P42345 GTEx:  ENSG00000198793

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0AN (Subject of Investigation/LOI)	C [auth A]	(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-[(~{E})-2-(2-chlorophenyl)ethenyl]-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one C28 H26 Cl3 N3 O3 S LZVLUVFCVSNKDX-MGLWIZITSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.238 
• R-Value Work: 0.192 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.912	α = 90
b = 64.68	β = 90
c = 93.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Meyners, C., Deutscher, R.C.E., Hausch, F.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	03ZU1109EB
German Research Foundation (DFG)	Germany	HA5556

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection