 Download MendeleyCrystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments
Grum-Tokars, V.L., Minasov, G., Roy, S.M., Anderson, W.F., Watterson, D.M.To be published.
4YPD | pdb_00004ypd
Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine
- PDB DOI: https://doi.org/10.2210/pdb4YPD/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2015-03-12 Released: 2015-05-13 
- Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.177 (Depositor), 0.190 (DCC) 
- R-Value Work: 0.155 (Depositor), 0.160 (DCC) 
- R-Value Observed: 0.156 (Depositor) 
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
This is version 1.3 of the entry. See complete history. 
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Death-associated protein kinase 1 | 294 | Homo sapiens | Mutation(s): 0  Gene Names: DAPK1, DAPK EC: 2.7.11.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53355 (Homo sapiens) Explore P53355  Go to UniProtKB:  P53355 | |||||
PHAROS:  P53355 GTEx:  ENSG00000196730  | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P53355 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| DKG Query on DKG | D [auth A] | 4-methylpyridazine C5 H6 N2 AIKUBOPKWKZULG-UHFFFAOYSA-N |  | ||
| CL Query on CL | B [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free:  0.177 (Depositor), 0.190 (DCC) 
- R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
- R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.853 | α = 90 |
| b = 62.511 | β = 90 |
| c = 88.193 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-05-13  Deposition Author(s): Grum-Tokars, V.L., Minasov, G., Roy, S.M., Anderson, W.F., Watterson, D.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute on Aging (NIH/NIA) | United States | U01AG043415 |
Revision History (Full details and data files)
- Version 1.0: 2015-05-13
Type: Initial release - Version 1.1: 2017-09-06
Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy - Version 1.2: 2019-12-18
Changes: Author supporting evidence - Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description
