6Y8M | pdb_00006y8m

Fragment bikinin bound to Interleukin 1 beta

PDB DOI: https://doi.org/10.2210/pdb6Y8M/pdb

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

Deposited: 2020-03-05 Released: 2020-03-18
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: 1.90 Å
R-Value Free:
0.222 (Depositor), 0.221 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6Y8M

Ligand Structure Quality Assessment

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

Literature

Fragment bikinin bound to Interleukin 1 beta

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

To be published.

Macromolecule Content

Total Structure Weight: 18.04 kDa
Atom Count: 1,308
Modeled Residue Count: 149
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
SX2 (Subject of Investigation/LOI) Query on SX2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	4-[(5-bromopyridin-2-yl)amino]-4-oxobutanoic acid C₉ H₉ Br N₂ O₃ XFYYQDHEDOXWGA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [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: 1.90 Å
R-Value Free: 0.222 (Depositor), 0.221 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.795	α = 90
b = 54.795	β = 90
c = 75.218	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

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: 2020-03-18
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.