Download MendeleyCrystal Structure Analysis of the Human Leukocyte Antigen B*46:01
Liu, J.X.To be published.
4LCY | pdb_00004lcy
4LCY | pdb_00004lcy
Crystal structure of HLA-b46 at 1.6 angstrom resolution
- PDB DOI: https://doi.org/10.2210/pdb4LCY/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Homo sapiens, dengue virus type 1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-06-24 Released: 2014-06-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.201 (Depositor), 0.206 (DCC)
- R-Value Work: 0.172 (Depositor), 0.179 (DCC)
- R-Value Observed: 0.174 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
Macromolecule Content
- Total Structure Weight: 89.6 kDa
- Atom Count: 7,457
- Modeled Residue Count: 766
- Deposited Residue Count: 766
- Unique protein chains: 3
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HLA class I histocompatibility antigen, B-46 alpha chain | A, D [auth F] | 274 | Homo sapiens | Mutation(s): 0 Gene Names: HLA, HLA-B, HLAB |  |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P01889 GTEx: ENSG00000234745 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01889 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Find similar proteins by:
| 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-2-microglobulin | B, E [auth H] | 100 | Homo sapiens | Mutation(s): 0 Gene Names: B2M, BETA 2 MICROGLOBULIN, CDABP0092, HDCMA22P |  |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P61769 GTEx: ENSG00000166710 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| dengue1 poly peptide | C, F [auth J] | 9 | dengue virus type 1 | Mutation(s): 0 |  |
UniProt | |||||
Entity Groups | |||||
| UniProt Group | P17763 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Download:Ideal Coordinates CCD File | G [auth A] H [auth A] I [auth B] J [auth F] K [auth F] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.201 (Depositor), 0.206 (DCC)
- R-Value Work: 0.172 (Depositor), 0.179 (DCC)
- R-Value Observed: 0.174 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.95 | α = 90 |
| b = 89.73 | β = 98.45 |
| c = 94.62 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2014-06-25 Deposition Author(s): Liu, J.X.
Revision History (Full details and data files)
- Version 1.0: 2014-06-25
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-03-20
Changes: Source and taxonomy - Version 1.3: 2024-11-20
Changes: Structure summary
