Download MendeleyCrystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235
Yoshida, K., Corper, A.L., Puckett, C., Sim, J., Valerie, M.-D., Jabri, B., Wilson, I.A., Teyton, L.To be published.
3CUP
Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235
- PDB DOI: https://doi.org/10.2210/pdb3CUP/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Drosophila melanogaster
- Mutation(s): No
- Deposited: 2008-04-16 Released: 2009-04-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.09 Å
- R-Value Free: 0.286
- R-Value Work: 0.232
- R-Value Observed: 0.235
Starting Model: experimental
View more details
This is version 2.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| H-2 class II histocompatibility antigen, A-D alpha chain | 190 | Mus musculus | Mutation(s): 0 Gene Names: H2-Aa |  | |
UniProt | |||||
Find proteins for P04228 (Mus musculus) Explore P04228 Go to UniProtKB: P04228 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04228 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MHC class II H2-IA-beta chain linked to GAD221-235 peptide | 222 | Mus musculus | Mutation(s): 0 EC: 4.1.1.15 |  | |
UniProt | |||||
Find proteins for Q31135 (Mus musculus) Explore Q31135 Go to UniProtKB: Q31135 | |||||
Find proteins for Q05683 (Rattus norvegicus) Explore Q05683 Go to UniProtKB: Q05683 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q31135Q05683 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | D [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | C [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: 3.09 Å
- R-Value Free: 0.286
- R-Value Work: 0.232
- R-Value Observed: 0.235
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.832 | α = 90 |
| b = 55.832 | β = 90 |
| c = 338.834 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
Entry History
Deposition Data
- Released Date: 2009-04-21 Deposition Author(s): Corper, A.L., Yoshida, K., Teyton, L., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2009-04-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2017-06-28
Changes: Advisory, Atomic model, Database references, Derived calculations, Refinement description, Source and taxonomy - Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.2: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.3: 2024-10-09
Changes: Structure summary
