3QD6
Crystal structure of the CD40 and CD154 (CD40L) complex
- PDB DOI: https://doi.org/10.2210/pdb3QD6/pdb
- Classification: CYTOKINE/CYTOKINE RECEPTOR
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No
- Deposited: 2011-01-18 Released: 2011-02-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.298
- R-Value Work: 0.245
- R-Value Observed: 0.245
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 |
| CD40 ligand | 149 | Homo sapiens | Mutation(s): 0 Gene Names: CD154, CD40L |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P29965 (Homo sapiens) Explore P29965 Go to UniProtKB: P29965 | |||||
PHAROS: P29965 GTEx: ENSG00000102245 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P29965 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tumor necrosis factor receptor superfamily member 5 | G [auth R], H [auth S], I [auth T], J [auth U] | 177 | Homo sapiens | Mutation(s): 0 Gene Names: CD40 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P25942 (Homo sapiens) Explore P25942 Go to UniProtKB: P25942 | |||||
PHAROS: P25942 GTEx: ENSG00000101017 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P25942 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | K [auth A] L [auth B] M [auth C] N [auth D] O [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.298
- R-Value Work: 0.245
- R-Value Observed: 0.245
- Space Group: P 65
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 133.212 | α = 90 |
| b = 133.212 | β = 90 |
| c = 211.151 | γ = 120 |
| Software Name | Purpose |
|---|---|
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
Entry History
Deposition Data
- Released Date: 2011-02-02 Deposition Author(s): Lee, J.-O., Kim, Y.J., Song, D.H., Kim, H.M., Park, B.S.
Revision History (Full details and data files)
- Version 1.0: 2011-02-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2012-03-21
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
