6Z2C | pdb_00006z2c

Engineered lipocalin C3A5 in complex with a transition state analog

• PDB DOI: https://doi.org/10.2210/pdb6Z2C/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-15 Released: 2021-05-26 
• Deposition Author(s): Skerra, A., Eichinger, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structure of an engineered lipocalin that catalyzes a Diels-Alder reaction

Eichinger, A., Skerra, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.91 kDa 
• Atom Count: 4,718 
• Modeled Residue Count: 531 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, B, C	188	Homo sapiens	Mutation(s): 21  Gene Names: LCN2, HNL, NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188  Go to UniProtKB:  P80188
PHAROS:  P80188 GTEx:  ENSG00000148346

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q5E (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	1,7,8,9,10,10-hexachloro-4-carboxypentyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-3,5-dione C15 H13 Cl6 N O4 JIUILXIUOXTHCP-ZPAAZFHLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.385	α = 90
b = 39.034	β = 120
c = 96.385	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Skerra, A., Eichinger, A.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary