6Y6O | pdb_00006y6o

Structure of mature activin A with small molecule 42

• PDB DOI: https://doi.org/10.2210/pdb6Y6O/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-26 Released: 2021-02-03 
• Deposition Author(s): McLoughlin, J.D., Brear, P.B., Reinhardt, T., Spring, D.R., Hyvonen, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.254 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion

Kidd, S.L., Fowler, E., Reinhardt, T., Compton, T., Mateu, N., Newman, H., Bellini, D., Talon, R., McLoughlin, J., Krojer, T., Aimon, A., Bradley, A., Fairhead, M., Brear, P., Diaz-Saez, L., McAuley, K., Sore, H.F., Madin, A., O'Donovan, D.H., Huber, K.V.M., Hyvonen, M., Dowson, C.G., Spring, D.R.

(2020) Chem Sci 11: 10792-10801

• DOI: https://doi.org/10.1039/D0SC01232G

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 26.72 kDa 
• Atom Count: 1,876 
• Modeled Residue Count: 226 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibin beta A chain	A, B	116	Homo sapiens	Mutation(s): 0  Gene Names: INHBA
UniProt & NIH Common Fund Data Resources
Find proteins for P08476 (Homo sapiens) Explore P08476  Go to UniProtKB:  P08476
PHAROS:  P08476 GTEx:  ENSG00000122641

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OCK (Subject of Investigation/LOI)	G [auth A]	(3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione C15 H20 N2 O2 QTYBGLRTPWRNRA-OAHLLOKOSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.254 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.05	α = 90
b = 96.938	β = 90
c = 117.242	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): McLoughlin, J.D., Brear, P.B., Reinhardt, T., Spring, D.R., Hyvonen, M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary