1A6A
THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
- PDB DOI: https://doi.org/10.2210/pdb1A6A/pdb
- Classification: COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 1998-02-22 Released: 1998-05-27 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.325 
- R-Value Work: 0.246 
- R-Value Observed: 0.246 
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 | 176 | Homo sapiens | Mutation(s): 0  | ||
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-1 beta chain | 187 | 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 |
HLA class II histocompatibility antigen, gamma chain | 15 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233 | |||||
PHAROS:  P04233 GTEx:  ENSG00000019582  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04233 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A], E [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: 2.75 Å
- R-Value Free: 0.325 
- R-Value Work: 0.246 
- R-Value Observed: 0.246 
- Space Group: P 32 1 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.45 | α = 90 |
b = 78.45 | β = 90 |
c = 159.1 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
ROTAVATA/AGROVATA | data reduction |
AMoRE | phasing |
X-PLOR | refinement |
CCP4 | data scaling |
ROTAVATA | data scaling |
Entry History 
Deposition Data
- Released Date: 1998-05-27  Deposition Author(s): Ghosh, P., Amaya, M., Mellins, E., Wiley, D.C.
Revision History (Full details and data files)
- Version 1.0: 1998-05-27
Type: Initial release - Version 1.1: 2008-03-24
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, Refinement description, Structure summary - Version 1.4: 2023-08-02
Changes: Advisory, Database references, Refinement description, Structure summary