8J5G

Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate

PDB DOI: https://doi.org/10.2210/pdb8J5G/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. ATCC 700974
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-22 Released: 2024-04-24
Deposition Author(s): Ushimaru, R., Mori, T., Liu, H.-w., Abe, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.169

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate

Ushimaru, R., Mori, T., Liu, H.-w., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 27.84 kDa
Atom Count: 2,183
Modelled Residue Count: 238
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyadenosine/deoxycytidine kinase	A	247	Streptomyces sp. ATCC 700974	Mutation(s): 1
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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TT9 (Subject of Investigation/LOI) Query on TT9 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-2-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl] phosphono hydrogen phosphate C₉ H₁₅ N₃ O₁₁ P₂ S KEAXZHZTGMHPPH-AYHNYZOXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.415	α = 90
b = 78.344	β = 90
c = 83.414	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-04-24
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.