3BX8 | pdb_00003bx8

Engineered Human Lipocalin 2 (LCN2), apo-form

• PDB DOI: https://doi.org/10.2210/pdb3BX8/pdb

• Classification: DE NOVO PROTEIN, PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-11 Released: 2009-01-20 
• Deposition Author(s): Schonfeld, D.L., Chatwell, L., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.282 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.265 (DCC) 

Starting Model: experimental

Literature

High affinity molecular recognition and functional blockade of CTLA-4 by an engineered human lipocalin

Schonfeld, D.L., Matschiner, G., Chatwell, L., Trentmann, S., Schlehuber, S., Hohlbaum, A., Skerra, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.25 kDa 
• Atom Count: 11,039 
• Modeled Residue Count: 1,310 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENGINEERED HUMAN LIPOCALIN 2	A, B, C, D, E, F, G, H	178	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE5	J [auth B], K [auth C], L [auth D], N [auth F], P [auth H]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
1PE	I [auth A], M [auth E], O [auth G]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.282 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.265 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.482	α = 110.77
b = 92.861	β = 90
c = 98.825	γ = 109.36

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Schonfeld, D.L., Chatwell, L., Skerra, A.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary