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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.238 (Depositor), 0.238 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fragment KCL_I013 in complex with IL-1-beta

De Nicola, G.F., Nichols, C.E.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGE (Subject of Investigation/LOI) Query on OGE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-(5-bromanylpyridin-2-yl)-3-(2-hydroxyethyl)urea C₈ H₁₀ Br N₃ O₂ DWHYNYBZZGQFNY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.238 (Depositor), 0.238 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

De Nicola, G.F.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.