4LHU
Crystal Structure of 9C2 TCR bound to CD1d
- PDB DOI: https://doi.org/10.2210/pdb4LHU/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni, Homo sapiens
- Mutation(s): No 
- Deposited: 2013-07-01 Released: 2013-10-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.87 Å
- R-Value Free: 0.243 
- R-Value Work: 0.206 
- R-Value Observed: 0.208 
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 |
Antigen-presenting glycoprotein CD1d | 278 | 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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
9C2 TCR delta chain | C [auth D] | 236 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q6PJ56 (Homo sapiens) Explore Q6PJ56  Go to UniProtKB:  Q6PJ56 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6PJ56 | ||||
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 |
9C2 TCR gamma chain | D [auth G] | 251 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P0CF51 (Homo sapiens) Explore P0CF51  Go to UniProtKB:  P0CF51 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0CF51 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C], F [auth E] | 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 | G [auth F] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
JLS Query on JLS | K [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 | |||
NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BMA Query on BMA | I [auth A] | beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N | |||
CL Query on CL | L [auth G] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | J [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.87 Å
- R-Value Free: 0.243 
- R-Value Work: 0.206 
- R-Value Observed: 0.208 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 131.62 | α = 90 |
b = 152.69 | β = 90 |
c = 135.2 | γ = 90 |
Software Name | Purpose |
---|---|
SCALA | data scaling |
PHASER | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
XDS | data reduction |
BUSTER | refinement |
Entry History 
Deposition Data
- Released Date: 2013-10-02  Deposition Author(s): Uldrich, A.P., Le Nours, J., Pellicci, D.G., Gras, S., Rossjohn, J., Godfrey, D.I.
Revision History (Full details and data files)
- Version 1.0: 2013-10-02
Type: Initial release - Version 1.1: 2013-10-16
Changes: Database references - Version 1.2: 2013-11-06
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary