Download MendeleyStructure of HLA-B*40:02 in complex with the phosphorilated endogenous peptide REFpSKEPEL
Alpizar, A., Marcilla, M., Santiago, C.To be published.
5IEH
Structure of HLA-B*40:02 in complex with the phosphorylated endogenous peptide REF(p)SKEPEL
- PDB DOI: 10.2210/pdb5IEH/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-02-25 Released: 2016-12-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.183
- R-Value Work: 0.161
- R-Value Observed: 0.162
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| HLA class I histocompatibility antigen, B-40 alpha chain | A | 277 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-B, HLAB |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01889 (Homo sapiens) Explore P01889 Go to UniProtKB: P01889 | |||||
PHAROS: P01889 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01889 | ||||
Protein Feature ViewExpand | |||||
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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 | B | 100 | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61769 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Inner centromere protein | C | 9 | Homo sapiens | Mutation(s): 0 Gene Names: INCENP |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NQS7 (Homo sapiens) Explore Q9NQS7 Go to UniProtKB: Q9NQS7 | |||||
PHAROS: Q9NQS7 | |||||
Entity Groups | |||||
| UniProt Group | Q9NQS7 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | D [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SEP Query on SEP | C | L-PEPTIDE LINKING | C3 H8 N O6 P |  | SER |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.183
- R-Value Work: 0.161
- R-Value Observed: 0.162
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.044 | α = 90 |
| b = 82.249 | β = 90 |
| c = 110.084 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-12-07 Deposition Author(s): Alpizar, A., Marcilla, M., Santiago, C.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Spain | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-12-07
Type: Initial release - Version 1.1: 2019-10-16
Changes: Data collection
