Download Mendeleycrystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
Qin, M.M., Deng, H.Z., Yao, L.S.To be published.
8I3P
crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
- PDB DOI: https://doi.org/10.2210/pdb8I3P/pdb
- Classification: HYDROLASE
- Organism(s): Saccharomyces cerevisiae S288C
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2023-01-17 Released: 2024-01-24
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.161
- R-Value Work: 0.141
- R-Value Observed: 0.142
Starting Model: experimental
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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 |
| Cytosine deaminase | 198 | Saccharomyces cerevisiae S288C | Mutation(s): 0 Gene Names: FCY1 EC: 3.5.4.1 |  | |
UniProt | |||||
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12178 Go to UniProtKB: Q12178 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q12178 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OS0 (Subject of Investigation/LOI) Query on OS0 | C [auth A], F [auth B] | 4-oxidanyl-3,4-dihydro-1H-pyrimidin-2-one C4 H6 N2 O2 DEAAWXYGBWCVJW-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | D [auth A], G [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], H [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.161
- R-Value Work: 0.141
- R-Value Observed: 0.142
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.175 | α = 90 |
| b = 68.9 | β = 101.58 |
| c = 49.424 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHENIX | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-01-24 Deposition Author(s): Qin, M.M., Deng, H.Z., Yao, L.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 32201011 |
Revision History (Full details and data files)
- Version 1.0: 2024-01-24
Type: Initial release
