8J5F | pdb_00008j5f

Crystal structure of kinase AbmG in complex with cytidine and ADP

PDB DOI: https://doi.org/10.2210/pdb8J5F/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. ATCC 700974
Expression System: Escherichia coli
Mutation(s): No

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: 1.70 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Biosynthesis of the Thiofuranose Core in Albomycin Requires a Versatile Enzyme AbmG That Catalyzes Net Dehydration via Cryptic Phosphorylation

Zheng, Z., Ushimaru, R., Mori, T., Ruszczycky, M.W., Abe, I., Liu, H.W.

(2025) J Am Chem Soc 147: 34143-34149

DOI: https://doi.org/10.1021/jacs.5c12827

Macromolecule Content

Total Structure Weight: 28.08 kDa
Atom Count: 2,232
Modeled Residue Count: 238
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyadenosine/deoxycytidine kinase	A	247	Streptomyces sp. ATCC 700974	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CTN (Subject of Investigation/LOI) Query on CTN 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]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.97	α = 90
b = 78.986	β = 90
c = 83.332	γ = 90

Software Package:

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

Structure Validation

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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
Version 1.1: 2025-11-05
Changes: Database references, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.