Download MendeleyCrystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine
Ushimaru, R., Mori, T., Liu, H.-w., Abe, I.To be published.
8J5H
Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine
- PDB DOI: https://doi.org/10.2210/pdb8J5H/pdb
- Classification: TRANSFERASE
- Organism(s): Streptomyces sp. ATCC 700974
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2023-04-22 Released: 2024-04-24
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.190
- R-Value Work: 0.174
- R-Value Observed: 0.174
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 |
| Deoxyadenosine/deoxycytidine kinase | 247 | Streptomyces sp. ATCC 700974 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A370RDE4 (Streptomyces sp. HB202) Explore A0A370RDE4 Go to UniProtKB: A0A370RDE4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A370RDE4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TV0 (Subject of Investigation/LOI) Query on TV0 | B [auth A] | 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4,5-tris(oxidanyl)thiolan-2-yl]pyrimidin-2-one C9 H13 N3 O5 S NCKQSFKRXULRQX-AYHNYZOXSA-N |  | ||
| NO3 Query on NO3 | C [auth A] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.190
- R-Value Work: 0.174
- R-Value Observed: 0.174
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.152 | α = 90 |
| b = 77.572 | β = 90 |
| c = 83.945 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-04-24 Deposition Author(s): Ushimaru, R., Mori, T., Liu, H.-w., Abe, I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-04-24
Type: Initial release
