Download MendeleyHLA-B*15:02 complexed with a synthetic peptide
Schutte, R.J., Li, D., Ostrov, D.A.To be published.
6VB5
HLA-B*15:02 complexed with a synthetic peptide
- PDB DOI: https://doi.org/10.2210/pdb6VB5/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-12-18 Released: 2020-11-25
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.224
- R-Value Work: 0.171
- R-Value Observed: 0.174
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
Currently 6VB5 does not have a validation slider image.
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MHC class I antigen | 276 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-B |  | |
UniProt | |||||
Find proteins for F4NBQ8 (Homo sapiens) Explore F4NBQ8 Go to UniProtKB: F4NBQ8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F4NBQ8 | ||||
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 |
| Beta-2-microglobulin | 99 | Homo sapiens | Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769 | |||||
PHAROS: P61769 GTEx: ENSG00000166710 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Synthetic peptide THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR | 9 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | F [auth A], G [auth A], H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | D [auth A], J [auth C] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Query on NA | I [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.224
- R-Value Work: 0.171
- R-Value Observed: 0.174
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.825 | α = 90 |
| b = 81.277 | β = 90 |
| c = 109.43 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Structure Validation
Currently 6VB5 does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2020-11-25 Deposition Author(s): Schutte, R.J., Li, D., Ostrov, D.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1R01AI103348-01 |
Revision History (Full details and data files)
- Version 1.0: 2020-11-25
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
