6NIX
Crystal structure of Immune Receptor
- PDB DOI: https://doi.org/10.2210/pdb6NIX/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2019-01-01 Released: 2020-01-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235
- R-Value Work: 0.178
- R-Value Observed: 0.181
wwPDB Validation 3D Report Full Report
Currently 6NIX does not have a validation slider image.
This is version 1.2 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 II histocompatibility antigen, DR alpha chain | 189 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-DRA, HLA-DRA1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01903 (Homo sapiens) Explore P01903 Go to UniProtKB: P01903 | |||||
PHAROS: P01903 GTEx: ENSG00000204287 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01903 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HLA class II histocompatibility antigen, DRB1-4 beta chain | 200 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-DRB1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01911 (Homo sapiens) Explore P01911 Go to UniProtKB: P01911 | |||||
PHAROS: P01911 GTEx: ENSG00000196126 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01911 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Type II Collagen | 15 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02458 (Homo sapiens) Explore P02458 Go to UniProtKB: P02458 | |||||
PHAROS: P02458 GTEx: ENSG00000139219 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02458 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| B3P Query on B3P | F [auth B] | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | D [auth A], E [auth A], G [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235
- R-Value Work: 0.178
- R-Value Observed: 0.181
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.92 | α = 90 |
| b = 178.038 | β = 90 |
| c = 76.239 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Aimless | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Structure Validation
Currently 6NIX does not have a validation slider image.
Entry History
Deposition Data
- Released Date: 2020-01-22 Deposition Author(s): Ting, Y.T., Reid, H.H., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2020-01-22
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
