4P2O
Crystal structure of the 2B4 TCR in complex with 2A/I-Ek
- PDB DOI: https://doi.org/10.2210/pdb4P2O/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, synthetic construct
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2014-03-04 Released: 2014-05-21 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.245 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
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 |
H-2 class II histocompatibility antigen, E-K alpha chain | 204 | Mus musculus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P04224 (Mus musculus) Explore P04224  Go to UniProtKB:  P04224 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04224 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MHC class II E-beta-k | 236 | Mus musculus | Mutation(s): 0  Gene Names: H2-Eb1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q31163 (Mus musculus) Explore Q31163  Go to UniProtKB:  Q31163 | |||||
IMPC:  MGI:95901 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q31163 | ||||
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 |
2B4 T-cell receptor alpha chain | 220 | Mus musculus | 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 |
2B4 T-cell receptor beta chain | 255 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
2A peptide | E [auth P] | 22 | synthetic construct | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | F [auth E] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G63564LA GlyCosmos:  G63564LA |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], H [auth C], I [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.245 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 239.936 | α = 90 |
b = 60.176 | β = 104.33 |
c = 78.359 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-05-21  Deposition Author(s): Birnbaum, M.E., Ozkan, E., Garcia, K.C.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2014-05-21
Type: Initial release - Version 1.1: 2014-06-11
Changes: Database references - Version 1.2: 2015-01-14
Changes: Database references - Version 1.3: 2015-02-25
Changes: Derived calculations - Version 2.0: 2017-09-20
Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary - Version 2.1: 2017-11-01
Changes: Author supporting evidence - Version 2.2: 2019-12-25
Changes: Author supporting evidence, Data collection - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary - Version 3.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary