5R7W | pdb_00005r7w

PanDDA analysis group deposition of ground-state model of INTERLEUKIN-1 BETA

PDB DOI: https://doi.org/10.2210/pdb5R7W/pdb
Deposition Group: G_1002138 (ground state) | Explore G_1002138

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

Deposited: 2020-03-02 Released: 2020-04-22
Deposition Author(s): De Nicola, G.F., Nichols, C.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.203 (Depositor), 0.211 (DCC)
R-Value Work:
0.187 (Depositor), 0.197 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5R7W

This is version 1.2 of the entry. See complete history.

Literature

PanDDA analysis group deposition of ground-state model

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

To be published.

Macromolecule Content

Total Structure Weight: 17.59 kDa
Atom Count: 1,411
Modeled Residue Count: 152
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.203 (Depositor), 0.211 (DCC)
R-Value Work: 0.187 (Depositor), 0.197 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.572	α = 90
b = 54.572	β = 90
c = 75.836	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

De Nicola, G.F.

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2026-02-18
Changes: Refinement description, Structure summary

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.