3X3F
TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2
- PDB DOI: https://doi.org/10.2210/pdb3X3F/pdb
- Classification: APOPTOSIS/IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No
- Deposited: 2015-01-20 Released: 2015-12-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.224
- R-Value Work: 0.186
- R-Value Observed: 0.188
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 |
| Heavy chain of KMTR2 | A [auth H] | 229 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 |
| Light chain of KMTR2 | B [auth L] | 214 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tumor necrosis factor receptor superfamily member 10B | C [auth A] | 142 | Homo sapiens | Mutation(s): 0 Gene Names: DR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O14763 (Homo sapiens) Explore O14763 Go to UniProtKB: O14763 | |||||
PHAROS: O14763 GTEx: ENSG00000120889 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O14763 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| GOL Query on GOL | F [auth L], G [auth L], H [auth L], I [auth L], J [auth L] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.224
- R-Value Work: 0.186
- R-Value Observed: 0.188
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 144.974 | α = 90 |
| b = 151.563 | β = 90 |
| c = 65.044 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2015-12-23 Deposition Author(s): Tamada, T.
Revision History (Full details and data files)
- Version 1.0: 2015-12-23
Type: Initial release - Version 1.1: 2015-12-30
Changes: Derived calculations - Version 1.2: 2018-10-17
Changes: Data collection, 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: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
