1YMM
TCR/HLA-DR2b/MBP-peptide complex
- PDB DOI: https://doi.org/10.2210/pdb1YMM/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): Yes 
- Deposited: 2005-01-21 Released: 2005-05-03 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.318 
- R-Value Work: 0.274 
- R-Value Observed: 0.276 
This is version 1.4 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 |
HLA class II histocompatibility antigen, DR alpha chain | 191 | Homo sapiens | Mutation(s): 0  Gene Names: HLA-DRA | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903 | |||||
PHAROS:  P01903 GTEx:  ENSG00000204287  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01903 | ||||
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 |
HLA class II histocompatibility antigen, DR beta chain | 198 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911 | |||||
PHAROS:  P01911 GTEx:  ENSG00000196126  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01911 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MBP peptide | 23 | Homo sapiens | Mutation(s): 0  Gene Names: MBP | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02686 (Homo sapiens) Explore P02686  Go to UniProtKB:  P02686 | |||||
PHAROS:  P02686 GTEx:  ENSG00000197971  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02686 | ||||
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 |
T cell receptor alpha chain | 207 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848 | |||||
PHAROS:  P01848 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01848 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
T-cell receptor beta chain | 249 | Homo sapiens | Mutation(s): 2  | ||
UniProt | |||||
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01850 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.318 
- R-Value Work: 0.274 
- R-Value Observed: 0.276 
- Space Group: F 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 137.34 | α = 90 |
b = 212.62 | β = 90 |
c = 278.22 | γ = 90 |
Software Name | Purpose |
---|---|
SCALEPACK | data scaling |
CNS | refinement |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2005-05-03  Deposition Author(s): Hahn, M., Nicholson, M.J., Pyrdol, J., Wucherpfennig, K.W.
Revision History (Full details and data files)
- Version 1.0: 2005-05-03
Type: Initial release - Version 1.1: 2007-10-16
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.4: 2021-10-20
Changes: Advisory, Database references, Structure summary