4GS7

Structure of the Interleukin-15 quaternary complex

PDB DOI: https://doi.org/10.2210/pdb4GS7/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): Yes

Deposited: 2012-08-27 Released: 2012-11-07
Deposition Author(s): Ring, A.M., Ozkan, E., Feng, D., Garcia, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.227
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 71.8 kDa
Atom Count: 5,053
Modelled Residue Count: 573
Deposited Residue Count: 605
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-15	A	116	Homo sapiens	Mutation(s): 0 Gene Names: IL15
UniProt & NIH Common Fund Data Resources
Find proteins for P40933 (Homo sapiens) Explore P40933 Go to UniProtKB: P40933
PHAROS: P40933 GTEx: ENSG00000164136
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40933
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit beta	B	217	Homo sapiens	Mutation(s): 3 Gene Names: IL2RB
UniProt & NIH Common Fund Data Resources
Find proteins for P14784 (Homo sapiens) Explore P14784 Go to UniProtKB: P14784
PHAROS: P14784 GTEx: ENSG00000100385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14784
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	C	203	Homo sapiens	Mutation(s): 1 Gene Names: IL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for P31785 (Homo sapiens) Explore P31785 Go to UniProtKB: P31785
PHAROS: P31785 GTEx: ENSG00000147168
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31785
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-15 receptor subunit alpha	D	69	Homo sapiens	Mutation(s): 0 Gene Names: IL15RA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13261 (Homo sapiens) Explore Q13261 Go to UniProtKB: Q13261
PHAROS: Q13261 GTEx: ENSG00000134470
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13261
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C]	I [auth C], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C]	H [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.227
R-Value Work: 0.182
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.949	α = 90
b = 74.61	β = 90
c = 129.211	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references
Version 1.2: 2012-12-05
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary