6ULB | pdb_00006ulb

Sex Hormone-binding globulin mutant E176K in complex with Danazol

• PDB DOI: https://doi.org/10.2210/pdb6ULB/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-07 Released: 2020-10-21 
• Deposition Author(s): Round, P.W., Das, S., Van Petegem, F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical analyses of danazol interactions with sex hormone-binding globulin and effects on androgen action

Round, P.W., Das, S., Van Petegem, F., Hammond, G.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.99 kDa 
• Atom Count: 1,510 
• Modeled Residue Count: 171 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sex hormone-binding globulin	A	205	Homo sapiens	Mutation(s): 1  Gene Names: SHBG
UniProt & NIH Common Fund Data Resources
Find proteins for P04278 (Homo sapiens) Explore P04278  Go to UniProtKB:  P04278
PHAROS:  P04278 GTEx:  ENSG00000129214

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QA1 (Subject of Investigation/LOI)	C [auth A]	Danazol C22 H27 N O2 POZRVZJJTULAOH-LHZXLZLDSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QA1	BindingDB:  6ULB	Kd: 6.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.007	α = 90
b = 52.007	β = 90
c = 149.238	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Round, P.W., Das, S., Van Petegem, F.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary