9E2T | pdb_00009e2t

Structure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg

PDB DOI: https://doi.org/10.2210/pdb9E2T/pdb

Classification: DE NOVO PROTEIN/IMMUNE SYSTEM
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): Yes

Deposited: 2024-10-22 Released: 2025-09-24
Deposition Author(s): Abhiraman, G.C., Jude, K.M., Garcia, K.C.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

De novo mimetic protein of interleukin-21 shows outstanding therapeutic efficacy in cancer.

Chun, J.H., Zhangxu, K., Roy, S., Abhiraman, G.C., Garcia, K.C., Dougan, S.K., Leonard, W., Dougan, M., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 197.5 kDa
Atom Count: 13,255
Modeled Residue Count: 1,591
Deposited Residue Count: 1,662
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
21h10	A, D, G, I	102	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-21 receptor	B, E, H, J	212	Homo sapiens	Mutation(s): 4 Gene Names: IL21R, NILR, UNQ3121/PRO10273
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBE5 (Homo sapiens) Explore Q9HBE5 Go to UniProtKB: Q9HBE5
PHAROS: Q9HBE5 GTEx: ENSG00000103522
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HBE5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E Focus chain H Focus chain J	Go to GlyGen: Q9HBE5-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	C, F	203	Homo sapiens	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain F	Go to GlyGen: P31785-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth H] SDF format, chain Z [auth J] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth H] MOL2 format, chain Z [auth J] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth H] mmCIF format, chain Z [auth J]	K [auth B] N [auth C] O [auth C] P [auth C] T [auth E] K [auth B], N [auth C], O [auth C], P [auth C], T [auth E], V [auth F], W [auth F], X [auth H], Z [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth H] Focus chain Z [auth J] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth H] Focus chain Z [auth J]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth E] SDF format, chain Y [auth H] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Y [auth H] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Y [auth H]	AA [auth J] BA [auth J] L [auth B] M [auth B] Q [auth C] AA [auth J], BA [auth J], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], U [auth E], Y [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth E] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth E] Focus chain Y [auth H]