6CQN
Crystal structure of F5 TCR -DR11-RQ13 peptide complex
- PDB DOI: https://doi.org/10.2210/pdb6CQN/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, HIV-1 M:B_HXB2R
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-03-15 Released: 2018-06-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.251 
- R-Value Work: 0.196 
- R-Value Observed: 0.199 
This is version 1.3 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 class II histocompatibility antigen, DRB1-11 beta chain | 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  Gene Names: gag | ||
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 |
F5 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
F5 beta chain | 245 | Homo sapiens | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for A0A0G2JMB4 (Homo sapiens) Explore A0A0G2JMB4  Go to UniProtKB:  A0A0G2JMB4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0G2JMB4 | ||||
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 | F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | H [auth A], J [auth B], K [auth B], N [auth E] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
CL Query on CL | I [auth A], M [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | L [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.251 
- R-Value Work: 0.196 
- R-Value Observed: 0.199 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 75.317 | α = 90 |
b = 205.792 | β = 90 |
c = 70.229 | 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: 2018-06-27
Changes: Data collection, Database references, Structure summary - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary