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), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

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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): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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), 0.190 (DCC)
R-Value Work: 0.151 (Depositor), 0.150 (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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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
Version 1.1: 2025-11-05
Changes: Database references, Structure summary

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.