8UQF

Crystal structure of designed cortisol-binding protein hcy129_mpnn5

• PDB DOI: https://doi.org/10.2210/pdb8UQF/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-23 Released: 2024-11-20 
• Deposition Author(s): Pellock, S.J., Bera, A.
• Funding Organization(s): Other private, Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.243 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Starting Model: in silico

Literature

Small molecule binding and sensing with a designed protein family

Lee, G.R., Pellock, S.J., Norn, C., Tischer, D., Dauparas, J., Anischenko, I., Mercer, J.A.M., Kang, A., Bera, A., Nguyen, H., Goreshnik, I., Vafeados, D., Roullier, N., Han, H.L., Coventry, B., Liu, D.R., Yeh, A.H.W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.63 kDa 
• Atom Count: 2,155 
• Modelled Residue Count: 246 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed cortisol-binding protein hcy129_mpnn5	A, B	135	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCY (Subject of Investigation/LOI)	C [auth A], D [auth B]	(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione C21 H30 O5 JYGXADMDTFJGBT-VWUMJDOOSA-N
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.243 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.016	α = 90
b = 48.609	β = 93.99
c = 56.438	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Pellock, S.J., Bera, A.

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Funding Organization	Location	Grant Number
Other private		--
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release