Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.95 kDa 
• Atom Count: 1499 
• Modelled Residue Count: 177 
• Deposited Residue Count: 177 
• Unique protein chains: 1

1KDK

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

• DOI: 10.2210/pdb1KDK/pdb

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


• Deposited: 2001-11-13 Released: 2002-05-15 
• Deposition Author(s): Grishkovskaya, I., Avvakumov, G.V., Hammond, G.L., Muller, Y.A.

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Experimental Data Snapshot

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

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

• PubMed: 12054810 
• DOI: 10.1016/S0022-2836(02)00169-9
• Primary Citation of Related Structures:  
  1KDM, 1KDK


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sex Hormone-Binding Globulin	A	177	Homo sapiens	Mutation(s): 0  Gene Names: SHBG
Find proteins for P04278 (Homo sapiens) Explore P04278  Go to UniProtKB:  P04278
NIH Common Fund Data Resources
PHAROS:  P04278 GTEx:  ENSG00000129214

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHT	A	5-ALPHA-DIHYDROTESTOSTERONE C19 H30 O2 NVKAWKQGWWIWPM-ABEVXSGRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DHT	Kd:  0.18000000715255737   nM  BindingDB
DHT	IC50:  3.799999952316284   nM  BindingDB
DHT	Kd :  0.8999999761581421   nM  PDBBind
DHT	Kd:  0.8999999761581421   nM  Binding MOAD

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 = 103.72	α = 90
b = 103.72	β = 90
c = 85.76	γ = 120

Software Package:

Software Name	Purpose
MAR	data collection
XDS	data reduction
REFMAC	refinement
MAR	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-13 
• Released Date: 2002-05-15 
Deposition Author(s): Grishkovskaya, I., Avvakumov, G.V., Hammond, G.L., Muller, Y.A.

Revision History  

• 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