6OEL

Engineered Fab bound to IL-4 receptor

PDB DOI: https://doi.org/10.2210/pdb6OEL/pdb

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

Deposited: 2019-03-27 Released: 2019-08-07
Deposition Author(s): Jude, K.M., Moraga, I., Spangler, J.B., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.256
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Currently 6OEL does not have a validation slider image.

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 111.32 kDa
Atom Count: 7,209
Modelled Residue Count: 922
Deposited Residue Count: 973
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
engineered Interleukin-4, RGA variant	A	129	Homo sapiens	Mutation(s): 8 Gene Names: IL4
UniProt & NIH Common Fund Data Resources
Find proteins for P05112 (Homo sapiens) Explore P05112 Go to UniProtKB: P05112
PHAROS: P05112 GTEx: ENSG00000113520
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05112
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-4 receptor subunit alpha	B	202	Homo sapiens	Mutation(s): 0 Gene Names: IL4R, IL4RA, 582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens) Explore P24394 Go to UniProtKB: P24394
PHAROS: P24394 GTEx: ENSG00000077238
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24394
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	C	189	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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
engineered Fab heavy chain	D [auth H]	229	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
engineered Fab light chain	E [auth L]	224	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	2		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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 I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	G [auth B], H [auth B], I [auth B], J [auth B], K [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain L [auth H] MOL2 format, chain L [auth H]	L [auth H]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain L [auth H] Interactions & Density Focus chain L [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.256
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: F 4₁ 3 2
Diffraction Data: https://doi.org/10.15785/SBGRID/652

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 328.1	α = 90
b = 328.1	β = 90
c = 328.1	γ = 90

Software Package:

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

Structure Validation

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Currently 6OEL does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI51321

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2019-08-21
Changes: Data collection, Database references
Version 1.2: 2019-10-02
Changes: Data collection, Database references
Version 1.3: 2019-12-18
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary