Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18216.31 
• Atom Count: 987 
• Residue Count: 162 
• Unique protein chains: 1

1XKI

Crystal structure of human tear lipocalin/von Ebners gland protein

• DOI: 10.2210/pdb1XKI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2004-09-29 Released: 2004-10-19 
• Deposition Author(s): Breustedt, D.A., Korndoerfer, I.P., Redl, B., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 

Literature

The 1.8-A crystal structure of human tear lipocalin reveals an extended branched cavity with capacity for multiple ligands

Breustedt, D.A., Korndoerfer, I.P., Redl, B., Skerra, A.

(2005) J.Biol.Chem. 280: 484-493

• PubMed: 15489503 
• DOI: 10.1074/jbc.M410466200


• PubMed Abstract: 
  

In contrast with earlier assumptions, which classified human tear lipocalin (Tlc) as an outlier member of the lipocalin protein family, the 1.8-A resolution crystal structure of the recombinant apoprotein confirms the typical eight-stranded antiparallel beta-barrel architecture with an alpha-helix attached to it. The fold of Tlc most closely resembles the bovine dander allergen Bos d 2, a well characterized prototypic lipocalin, but also reveals similarity with beta-lactoglobulin. However, compared with other lipocalin structures Tlc exhibits an extremely wide ligand pocket, whose entrance is formed by four partially disordered loops. The cavity deeply extends into the beta-barrel structure, where it ends in two distinct lobes. This unusual structural feature explains the known promiscuity of Tlc for various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampin and even to microbial siderophores. Notably, earlier findings of biological activity as a thiol protease inhibitor have no correspondence in the three-dimensional structure of Tlc, rather it appears that its proteolytic fragments could be responsible for this phenomenon. Hence, the present structural analysis sheds new light on the ligand binding activity of this functionally obscure but abundant human lipocalin.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Von Ebner's gland protein	A	162	Homo sapiens	Mutation(s): 2  Gene Names: LCN1 (VEGP)
Find proteins for P31025 (Homo sapiens) Go to Gene View: LCN1 Go to UniProtKB:  P31025

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 76.397	α = 90.00
b = 61.415	β = 129.71
c = 50.798	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-29 
• Released Date: 2004-10-19 
• Deposition Author(s): Breustedt, D.A., Korndoerfer, I.P., Redl, B., Skerra, A.

Revision History 

• Version 1.0: 2004-10-19
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance