7XCB | pdb_00007xcb

Crystal structure of the mouse interleukin-9

PDB DOI: https://doi.org/10.2210/pdb7XCB/pdb

Classification: CYTOKINE
Organism(s): Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-03-23 Released: 2023-03-29
Deposition Author(s): Kim, J.W., Lee, J.-O., Park, S.M.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.290 (Depositor), 0.287 (DCC)
R-Value Work:
0.241 (Depositor), 0.242 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the mouse interleukin-9

Kim, J.W., Lee, J.-O., Park, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 13.87 kDa
Atom Count: 958
Modeled Residue Count: 120
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-9	A	120	Mus musculus	Mutation(s): 0 Gene Names: Il9
UniProt & NIH Common Fund Data Resources
Find proteins for P15247 (Mus musculus) Explore P15247 Go to UniProtKB: P15247
IMPC: MGI:96563
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15247
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P15247-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		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: 3.40 Å
R-Value Free: 0.290 (Depositor), 0.287 (DCC)
R-Value Work: 0.241 (Depositor), 0.242 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.5	α = 90
b = 95.5	β = 90
c = 105.71	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019M3E5D6066058, 2017M3A9F6029753

Revision History (Full details and data files)

Version 1.0: 2023-03-29
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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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.