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

wwPDB Validation 3D Report Full Report

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]	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 R01GM133198.