3WO3
Crystal structure of IL-18 in complex with IL-18 receptor alpha
- PDB DOI: https://doi.org/10.2210/pdb3WO3/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli, Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2013-12-19 Released: 2014-12-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.10 Å
- R-Value Free: 0.222 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Interleukin-18 | 157 | Homo sapiens | Mutation(s): 0  Gene Names: IL18 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q14116 (Homo sapiens) Explore Q14116  Go to UniProtKB:  Q14116 | |||||
PHAROS:  Q14116 GTEx:  ENSG00000150782  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q14116 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Interleukin-18 receptor 1 | 312 | Homo sapiens | Mutation(s): 0  Gene Names: IL18R1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q13478 (Homo sapiens) Explore Q13478  Go to UniProtKB:  Q13478 | |||||
PHAROS:  Q13478 GTEx:  ENSG00000115604  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q13478 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | HA [auth h], M, Q | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-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 | N, W | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G34442SS GlyCosmos:  G34442SS GlyGen:  G34442SS |
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 | BA [auth b], GA [auth g], JA [auth j], KA [auth k], O | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | CA [auth c], EA [auth e], FA [auth f], IA [auth i], P, CA [auth c], EA [auth e], FA [auth f], IA [auth i], P, T, U, X | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | R | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC |
Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a], S | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | DA [auth d], LA [auth l], V | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Y | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC |
Entity ID: 11 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Z | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G00395TQ GlyCosmos:  G00395TQ GlyGen:  G00395TQ |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AB [auth D] CC [auth J] LB [auth F] MB [auth F] OA [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | AC [auth H] BB [auth D] BC [auth I] CB [auth D] DB [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.10 Å
- R-Value Free: 0.222 
- R-Value Work: 0.191 
- R-Value Observed: 0.192 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 135.49 | α = 90 |
b = 174.814 | β = 90 |
c = 183.398 | γ = 90 |
Software Name | Purpose |
---|---|
BSS | data collection |
PHASER | phasing |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-12-17  Deposition Author(s): Tsutsumi, N., Kimura, T., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato, Z., Tochio, H.
Revision History (Full details and data files)
- Version 1.0: 2014-12-17
Type: Initial release - Version 1.1: 2016-01-20
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 - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary