Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.30 kDa 
• Atom Count: 1583 
• Modelled Residue Count: 166 
• Deposited Residue Count: 174 
• Unique protein chains: 1

2HZQ

Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone

• DOI: 10.2210/pdb2HZQ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2006-08-09 Released: 2007-08-14 
• Deposition Author(s): Eichinger, A., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structural insight into the dual ligand specificity and mode of high density lipoprotein association of apolipoprotein d.

Eichinger, A., Nasreen, A., Kim, H.J., Skerra, A.

(2007) J Biol Chem 282: 31068-31075

• PubMed: 17699160 
• DOI: 10.1074/jbc.M703552200
• Primary Citation of Related Structures:  
  2HZR, 2HZQ


• PubMed Abstract: 
  

Human apolipoprotein D (ApoD) occurs in plasma associated with high density lipoprotein. Apart from the involvement in lipid metabolism, its binding activity for progesterone and arachidonic acid plays a role in cancer development and neurological diseases. The crystal structures of free ApoD and its complex with progesterone were determined at 1.8A resolution and reveal a lipocalin fold. The narrow, mainly uncharged pocket within the typical beta-barrel accommodates progesterone with its acetyl side chain oriented toward the bottom. The cavity adopts essentially the same shape in the absence of progesterone and allows complexation of arachidonic acid as another cognate ligand. Three of the four extended loops at the open end of the beta-barrel expose hydrophobic side chains, which is an unusual feature for lipocalins and probably effects association with the high density lipoprotein particle by mediating insertion into the lipid phase. This mechanism is in line with an unpaired Cys residue in the same surface region that can form a disulfide cross-link with apolipoprotein A-II.

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Organizational Affiliation: 

Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein D	A	174	Homo sapiens	Mutation(s): 10  Gene Names: APOD Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P05090 (Homo sapiens) Explore P05090  Go to UniProtKB:  P05090
PHAROS:  P05090 GTEx:  ENSG00000189058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STR (Subject of Investigation/LOI)	B [auth A]	PROGESTERONE C21 H30 O2 RJKFOVLPORLFTN-LEKSSAKUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
STR	Kd:  1000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.206	α = 90
b = 49.206	β = 90
c = 144.126	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
REFMAC	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-08-09 
• Released Date: 2007-08-14 
Deposition Author(s): Eichinger, A., Skerra, A.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance