4WO4
The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition.
- PDB DOI: https://doi.org/10.2210/pdb4WO4/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2014-10-15 Released: 2014-11-26 
- Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
This is version 3.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d | 274 | Homo sapiens | Mutation(s): 0  Gene Names: CD1D | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813 | |||||
PHAROS:  P15813 GTEx:  ENSG00000158473  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P15813 | ||||
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 |
Beta-2-microglobulin | 100 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
TCR variable DELTA 1 CHAIN and TCR constant Alpha | 207 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
TCR variable BETA 2 (TRVB20) chain and TCR constant BETA | 245 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
JLS Query on JLS | H [auth A] | (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide C48 H93 N O9 QMLKBWVXCMTWOZ-WWHSRKRPSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.93 | α = 90 |
b = 79.25 | β = 90 |
c = 189.16 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-11-26  Deposition Author(s): Pellicci, D.G., Uldrich, A.P., Le Nours, J., Ross, F., Chabrol, E., Eckle, S.B.G., de Boer, R., Lim, R.T., McPherson, K., Besra, G., Howell, A.R., Moretta, L., McCluskey, J., Heemskerk, M.H.M., Gras, S., Rossjohn, J., Godfrey, D.I.
Funding Organization | Location | Grant Number |
---|---|---|
National Health and Medical Research Council (NHMRC, Australia) | Australia | -- |
Revision History (Full details and data files)
- Version 1.0: 2014-11-26
Type: Initial release - Version 1.1: 2014-12-17
Changes: Database references - Version 1.2: 2014-12-24
Changes: Database references - Version 2.0: 2017-09-13
Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary - Version 2.1: 2020-01-08
Changes: Author supporting evidence, Data collection - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary