Download MendeleyPrediction of Immunogenicity of altered-peptide ligands to HIV bound to MHC
Collins, E.J., Lee, H.Y.To be published.
3V5K
HLA2.1 KVAELVWFL
- PDB DOI: https://doi.org/10.2210/pdb3V5K/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-12-16 Released: 2012-12-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.228
- R-Value Work: 0.185
- R-Value Observed: 0.188
wwPDB Validation 3D Report Full Report
This is version 1.2 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, A-2 alpha chain | 275 | Homo sapiens | Mutation(s): 0 Gene Names: HLA*0201, HLA-A, HLAA |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439 | |||||
PHAROS: P04439 GTEx: ENSG00000206503 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04439 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-2-microglobulin | 100 | Homo sapiens | Mutation(s): 0 Gene Names: B2M, beta-2-microglobulin, 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 |
| HIV-based altered-peptide ligand KVAELVWFL | 9 | Homo sapiens | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for E0YFW1 (Human immunodeficiency virus type 1) Explore E0YFW1 Go to UniProtKB: E0YFW1 | |||||
Entity Groups | |||||
| UniProt Group | E0YFW1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | G [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.228
- R-Value Work: 0.185
- R-Value Observed: 0.188
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.773 | α = 90 |
| b = 87.078 | β = 90.04 |
| c = 79.683 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PHASER | phasing |
| BUSTER-TNT | refinement |
| PDB_EXTRACT | data extraction |
| MAR345dtb | data collection |
| DENZO | data reduction |
| BUSTER | refinement |
Entry History
Deposition Data
- Released Date: 2012-12-19 Deposition Author(s): Collins, E.J., Lee, H.Y.
Revision History (Full details and data files)
- Version 1.0: 2012-12-19
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary
