5L2K
Crystal structure of GEM42 TCR-CD1b-GMM complex
- PDB DOI: https://doi.org/10.2210/pdb5L2K/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens, Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2016-08-02 Released: 2016-11-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.239 
- R-Value Work: 0.218 
- R-Value Observed: 0.219 
This is version 1.3 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 |
T-cell surface glycoprotein CD1b | 300 | Homo sapiens | Mutation(s): 1  Gene Names: CD1B | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P29016 (Homo sapiens) Explore P29016  Go to UniProtKB:  P29016 | |||||
PHAROS:  P29016 GTEx:  ENSG00000158485  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P29016 | ||||
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 | 98 | 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 |
GEM42 TCR alpha chain | C [auth D] | 204 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
GEM42 TCR beta chain | D [auth E] | 243 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
70E Query on 70E | U [auth E] | 6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose C42 H82 O8 YOCZDGRJDQLKHW-GWLFWXKWSA-N | |||
6UL Query on 6UL | O [auth A] | TETRACOSYL PALMITATE C40 H80 O2 KKTAIMZGSAQXRE-UHFFFAOYSA-N | |||
NAG Query on NAG | E [auth A], F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CS Query on CS | R [auth D] | CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N | |||
SO4 Query on SO4 | H [auth A], I [auth A], J [auth A], Q [auth D], S [auth E] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
CL Query on CL | K [auth A], L [auth A], M [auth A], P [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | N [auth A], T [auth E] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.239 
- R-Value Work: 0.218 
- R-Value Observed: 0.219 
- Space Group: P 64 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 174.998 | α = 90 |
b = 174.998 | β = 90 |
c = 170.869 | γ = 120 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Entry History 
Deposition Data
- Released Date: 2016-11-16  Deposition Author(s): Gras, S., Shahine, A., Le Nours, J., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2016-11-16
Type: Initial release - Version 1.1: 2016-12-07
Changes: Other - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.3: 2023-10-04
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary