6CQQ
Crystal structure of F24 TCR -DR15-RQ13 peptide complex
- PDB DOI: https://doi.org/10.2210/pdb6CQQ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, HIV-1 M:B_HXB2R
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2018-03-16 Released: 2018-06-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.254
- R-Value Work: 0.207
- R-Value Observed: 0.209
This is version 1.4 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 | 182 | 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 | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HLA-DRB1 protein | 190 | 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 | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptide from Capsid protein p24 | 13 | HIV-1 M:B_HXB2R | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04585 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| F24 alpha chain | 205 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0A0B4J272 (Homo sapiens) Explore A0A0B4J272 Go to UniProtKB: A0A0B4J272 | |||||
PHAROS: A0A0B4J272 GTEx: ENSG00000211805 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0B4J272 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| F24 beta chain | 245 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9 Go to UniProtKB: A0A5B9 | |||||
PHAROS: A0A5B9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A5B9 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | K [auth A], O [auth F], P [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | N [auth E] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | Q [auth J] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | L [auth B], M [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.254
- R-Value Work: 0.207
- R-Value Observed: 0.209
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 76.339 | α = 90 |
| b = 203.273 | β = 109.16 |
| c = 100.245 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| XDS | data reduction |
| Aimless | data scaling |
Entry History
Deposition Data
- Released Date: 2018-06-06 Deposition Author(s): Farenc, C., Gras, S., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2018-06-06
Type: Initial release - Version 1.1: 2018-06-20
Changes: Data collection, Derived calculations - Version 1.2: 2018-06-27
Changes: Data collection, Database references, Structure summary - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
