2SEB
X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II
- PDB DOI: https://doi.org/10.2210/pdb2SEB/pdb
- Classification: COMPLEX (MHC CLASS II/SUPERANTIGEN)
- Organism(s): Homo sapiens, Staphylococcus aureus
- Expression System: Drosophila
- Mutation(s): No 
- Deposited: 1997-10-16 Released: 1998-01-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.280 
- R-Value Work: 0.229 
- R-Value Observed: 0.229 
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 | 181 | 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN | 192 | 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 | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ENTEROTOXIN TYPE B | C [auth D] | 239 | Staphylococcus aureus | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P01552 (Staphylococcus aureus) Explore P01552  Go to UniProtKB:  P01552 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01552 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PEPTIDE FROM COLLAGEN II | D [auth E] | 12 | Homo sapiens | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02458 (Homo sapiens) Explore P02458  Go to UniProtKB:  P02458 | |||||
PHAROS:  P02458 GTEx:  ENSG00000139219  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02458 | ||||
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 | 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: 2.50 Å
- R-Value Free: 0.280 
- R-Value Work: 0.229 
- R-Value Observed: 0.229 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.53 | α = 90 |
b = 100.28 | β = 90 |
c = 100.87 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 1998-01-28  Deposition Author(s): Dessen, A., Lawrence, C.M., Cupo, S., Zaller, D.M., Wiley, D.C.
Revision History (Full details and data files)
- Version 1.0: 1998-01-28
Type: Initial release - Version 1.1: 2008-03-25
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, Database references, Derived calculations, Structure summary - Version 1.4: 2023-08-09
Changes: Advisory, Database references, Refinement description, Structure summary