8RYS

Human IL-1beta, unliganded

PDB DOI: https://doi.org/10.2210/pdb8RYS/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-09 Released: 2024-03-06
Deposition Author(s): Rondeau, J.-M., Lehmann, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.221
R-Value Work: 0.206
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Ligandability assessment of IL-1beta by integrated hit identification approaches

Vulpetti, A., Rondeau, J.-M., Bellance, M.-H., Blank, J., Boesch, R., Boettcher, A., Bornancin, F., Buhr, S., Connor, L.E., Dumelin, C.E., Esser, O., Hediger, M., Hintermann, S., Hommel, U., Koch, E., Lapointe, G., Leder, L., Lehmann, S., Lehr, P., Meier, P., Muller, L., Ostermeier, D., Ramage, P., Schiebel-Haddad, S., Smith, A.B., Stojanovic, A., Velcicky, J., Yamamoto, R., Hurth, K.

To be published.

Macromolecule Content

Total Structure Weight: 17.49 kDa
Atom Count: 1,382
Modelled Residue Count: 150
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 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: 1.16 Å
R-Value Free: 0.221
R-Value Work: 0.206
R-Value Observed: 0.207
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.784	α = 90
b = 54.784	β = 90
c = 76.173	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-06
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.