Download MendeleyCryo-EM structure of human CDADC1 inactive mutant (E400A): trimer without a ligand
Slyvka, A., Rathore, I., Yang, R., Kanai, T., Lountos, G., Wang, Z., Skowronek, K., Czarnocki-Cieciura, M., Wlodawer, A., Bochtler, M.To be published.
9HFT | pdb_00009hft
Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with 5mdCTP bound in the active site
- PDB DOI: https://doi.org/10.2210/pdb9HFT/pdb
- EM Map EMD-52126: EMDB EMDataResource
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2024-11-18 Released: 2025-04-30
- Funding Organization(s): Foundation for Polish Science, Ministry of Science and Higher Education (Poland), National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.90 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: in silico
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wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| Cytidine and dCMP deaminase domain-containing protein 1 | 534 | Homo sapiens | Mutation(s): 1 Gene Names: CDADC1 EC: 3.5.4.5 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9BWV3 (Homo sapiens) Explore Q9BWV3 Go to UniProtKB: Q9BWV3 | |||||
PHAROS: Q9BWV3 GTEx: ENSG00000102543 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9BWV3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1I2I (Subject of Investigation/LOI) Query on A1I2I | I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] | [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C10 H18 N3 O13 P3 NGYHUCPPLJOZIX-UHFFFAOYSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | G [auth A] H [auth A] J [auth B] K [auth B] M [auth C] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.90 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Coot | |
| RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-04-30 Deposition Author(s): Slyvka, A., Rathore, I., Yang, R., Kanai, T., Lountos, G., Wang, Z., Skowronek, K., Czarnocki-Cieciura, M., Wlodawer, A., Bochtler, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Foundation for Polish Science | Poland | POIR.04.04.00-00-5D81/17-00 |
| Ministry of Science and Higher Education (Poland) | Poland | PPI/APM/2018/1/00034 |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | NIH Intramural Research Program |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | 75N91019D00024 |
Revision History (Full details and data files)
- Version 1.0: 2025-04-30
Type: Initial release
