6ULB

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.225
R-Value Work: 0.184
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04278
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QA1 (Subject of Investigation/LOI) Query on QA1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	Danazol C₂₂ H₂₇ N O₂ POZRVZJJTULAOH-LHZXLZLDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.225
R-Value Work: 0.184
R-Value Observed: 0.188
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

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Entry History & Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Van Petegem, F.

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

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.