6SP3

mouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 1

PDB DOI: https://doi.org/10.2210/pdb6SP3/pdb

Classification: CYTOKINE
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-08-30 Released: 2020-09-09
Deposition Author(s): Bloch, Y., Savvides, S.N.
Funding Organization(s): Research Foundation - Flanders

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.267
R-Value Work: 0.239
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7PUR

Literature

Around she goes: the structure of mouse Interleukin-12 p80

Bloch, Y., Savvides, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 80.98 kDa
Atom Count: 4,780
Modelled Residue Count: 603
Deposited Residue Count: 688
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-12 subunit beta	A, B	344	Mus musculus	Mutation(s): 0 Gene Names: Il12b
UniProt & NIH Common Fund Data Resources
Find proteins for P43432 (Mus musculus) Explore P43432 Go to UniProtKB: P43432
IMPC: MGI:96540
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43432
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	6		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.267
R-Value Work: 0.239
R-Value Observed: 0.241
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.8	α = 90
b = 176.14	β = 108.963
c = 54.37	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	12S0519N
Research Foundation - Flanders	Belgium	G0B4918N
Research Foundation - Flanders	Belgium	G0E1516N

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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.