6Y8I | pdb_00006y8i

Fragment KCL_I013 in complex with IL-1-beta

• PDB DOI: https://doi.org/10.2210/pdb6Y8I/pdb

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


• Deposited: 2020-03-05 Released: 2020-06-17 
• Deposition Author(s): De Nicola, G.F., Nichols, C.E.
• Funding Organization(s): British Heart Foundation, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Fragment KCL_I013 in complex with IL-1-beta

De Nicola, G.F., Nichols, C.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.75 kDa 
• Atom Count: 1,198 
• Modeled Residue Count: 147 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A	153	Homo sapiens	Mutation(s): 0  Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584 GTEx:  ENSG00000125538

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGE (Subject of Investigation/LOI)	C [auth A]	1-(5-bromanylpyridin-2-yl)-3-(2-hydroxyethyl)urea C8 H10 Br N3 O2 DWHYNYBZZGQFNY-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.79	α = 90
b = 54.79	β = 90
c = 75.57	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): De Nicola, G.F., Nichols, C.E.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	SP/14/2/30922, FS/14/29/30896
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_PC_17164

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description