3WO4
Crystal structure of the IL-18 signaling ternary complex
- PDB DOI: https://doi.org/10.2210/pdb3WO4/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: 0.232 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Interleukin-18 receptor accessory protein | 344 | Homo sapiens | Mutation(s): 0  Gene Names: IL18RAP | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O95256 (Homo sapiens) Explore O95256  Go to UniProtKB:  O95256 | |||||
PHAROS:  O95256 GTEx:  ENSG00000115607  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O95256 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
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 | F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G, J | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 8 | |||||
---|---|---|---|---|---|
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 | H | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | I | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | K [auth B], L [auth B], M [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | N [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.10 Å
- R-Value Free: 0.232 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 72.56 | α = 90 |
b = 111.56 | β = 90 |
c = 134.56 | γ = 90 |
Software Name | Purpose |
---|---|
UGUIS | data collection |
PHASER | phasing |
BUSTER | refinement |
HKL-2000 | data reduction |
HKL-2000 | 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