3MDY | pdb_00003mdy

Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189

• PDB DOI: https://doi.org/10.2210/pdb3MDY/pdb

• Classification: Transferase/isomerase
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-31 Released: 2010-05-19 
• Deposition Author(s): Chaikuad, A., Sanvitale, C., Mahajan, P., Daga, N., Cooper, C., Krojer, T., Alfano, I., Knapp, S., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189

Chaikuad, A., Sanvitale, C., Mahajan, P., Daga, N., Cooper, C., Krojer, T., Alfano, I., Knapp, S., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.55 kDa 
• Atom Count: 7,525 
• Modeled Residue Count: 858 
• Deposited Residue Count: 892 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone morphogenetic protein receptor type-1B	A, B [auth C]	337	Homo sapiens	Mutation(s): 0  Gene Names: BMPR1B EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for O00238 (Homo sapiens) Explore O00238  Go to UniProtKB:  O00238
PHAROS:  O00238 GTEx:  ENSG00000138696

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	C [auth B], D	109	Homo sapiens	Mutation(s): 0  Gene Names: 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
LDN	E [auth A], F [auth C]	4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline C25 H22 N6 CDOVNWNANFFLFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LDN	BindingDB:  3MDY	IC50: min: 0.94, max: 3800 (nM) from 9 assay(s)
		EC50: min: 48, max: 50 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.41	α = 90
b = 80.01	β = 90
c = 183.33	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Chaikuad, A., Sanvitale, C., Mahajan, P., Daga, N., Cooper, C., Krojer, T., Alfano, I., Knapp, S., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description