5B38
KIR3DL1*005 in complex with HLA-B*57:01
- PDB DOI: https://doi.org/10.2210/pdb5B38/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Enterobacteria phage L1, Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2016-02-12 Released: 2016-03-30 
- Funding Organization(s): National Health and Medical Research Council (Australia)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 
- R-Value Work: 0.196 
- R-Value Observed: 0.198 
This is version 1.5 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 I histocompatibility antigen, B-57 alpha chain | 276 | 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 GTEx:  ENSG00000234745  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01889 | ||||
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 | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
peptide from Ig kappa chain C region | 9 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834 | |||||
PHAROS:  P01834 | |||||
Entity Groups   | |||||
UniProt Group | P01834 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Killer cell immunoglobulin-like receptor 3DL1 | D [auth G] | 299 | Homo sapiens | Mutation(s): 2  Gene Names: KIR3DL1, CD158E, NKAT3, NKB1 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P43629 (Homo sapiens) Explore P43629  Go to UniProtKB:  P43629 | |||||
PHAROS:  P43629 GTEx:  ENSG00000167633  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P43629 | ||||
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 G], F [auth G], G | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 
- R-Value Work: 0.196 
- R-Value Observed: 0.198 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 51.557 | α = 95.2 |
b = 61.271 | β = 100.25 |
c = 66.365 | γ = 108.22 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-03-30  Deposition Author(s): Vivian, J.P., Rossjohn, J.
Funding Organization | Location | Grant Number |
---|---|---|
National Health and Medical Research Council (Australia) | Australia | 1099814 |
Revision History (Full details and data files)
- Version 1.0: 2016-03-30
Type: Initial release - Version 1.1: 2016-04-20
Changes: Database references - Version 1.2: 2016-05-18
Changes: Database references - Version 1.3: 2017-10-18
Changes: Author supporting evidence, Data collection, Database references, Derived calculations - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary