1KDK

THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site.

Grishkovskaya, I., Avvakumov, G.V., Hammond, G.L., Muller, Y.A.

(2002) J Mol Biol 318: 621-626

  • DOI: 10.1016/S0022-2836(02)00169-9
  • Primary Citation of Related Structures:  
    1KDK, 1KDM

  • PubMed Abstract: 

    • The crystal structure of human sex hormone-binding globulin (SHBG) has revealed how 5alpha-dihydrotestosterone intercalates between the two seven-stranded beta-sheets of its amino-terminal laminin G-like domain. However, a region of disorder (residues 130 to 135 of SHBG) was identified together with a zinc-binding site in immediate proximity to the steroid ...

    The crystal structure of human sex hormone-binding globulin (SHBG) has revealed how 5alpha-dihydrotestosterone intercalates between the two seven-stranded beta-sheets of its amino-terminal laminin G-like domain. However, a region of disorder (residues 130 to 135 of SHBG) was identified together with a zinc-binding site in immediate proximity to the steroid. It has been important to resolve the structure of this region because previous studies have suggested that these residues may contribute to steroid binding directly. Here, we present the 2.35 A and 1.7 A crystal structures of the amino-terminal LG domain of SHBG obtained from a tetragonal crystal form and by EDTA-soaking of a trigonal crystal form, respectively. In both of these new structures, residues Pro130 to Arg135 are now clearly visible. Substitution of the two residues (Leu131Gly and Lys134Ala) pointing towards the steroid has shown that only Leu131 contributes significantly to steroid binding. Rather than covering the steroid-binding pocket in an extended conformation, a 3(10) helical turn is formed by residues Leu131 to Lys134 in this segment. Unfolding of this secondary structure element can either facilitate the entry of the steroids into the binding site or modulate the important contribution that Leu131 makes to steroid binding. A comparison with previous structures supports the concept that zinc binding re-orients the side-chain of His136, and this residue serves as a lever causing disorder within the loop structure between Pro130 and Arg135.

    Organizational Affiliation: 

    Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, 13092 Berlin, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sex Hormone-Binding GlobulinA177Homo sapiensMutation(s): 0 
Gene Names: SHBG
UniProt & NIH Common Fund Data Resources
Find proteins for P04278 (Homo sapiens)
Explore P04278 
Go to UniProtKB:  P04278
PHAROS:  P04278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04278
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHT
Query on DHT
Download Ideal Coordinates CCD File 
B [auth A]5-ALPHA-DIHYDROTESTOSTERONE
C19 H30 O2
NVKAWKQGWWIWPM-ABEVXSGRSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DHT PDBBind:  1KDK Kd: 0.9 (nM) from 1 assay(s)
Binding MOAD:  1KDK Kd: 0.9 (nM) from 1 assay(s)
BindingDB:  1KDK Kd: 0.18 (nM) from 1 assay(s)
IC50: 3.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.72α = 90
b = 103.72β = 90
c = 85.76γ = 120
Software Package:
Software NamePurpose
MARdata collection
XDSdata reduction
REFMACrefinement
MARdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance