9MG2 | pdb_00009mg2

Structure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with sinefungin

PDB DOI: https://doi.org/10.2210/pdb9MG2/pdb

Classification: TRANSFERASE
Organism(s): Kluyveromyces lactis NRRL Y-1140
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-10 Released: 2025-07-09
Deposition Author(s): Nilson, D.J., Fedorov, E., Ghosh, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.219 (Depositor), 0.217 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic Sinefungin

Nilson, D.J., Schwer, B., Shuman, S., Almo, S.C.

(2025) Nucleic Acids Res

DOI: https://doi.org/10.1093/nar/gkaf538

Macromolecule Content

Total Structure Weight: 67.98 kDa
Atom Count: 5,249
Modeled Residue Count: 576
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA cap guanine-N(7) methyltransferase	A, B	289	Kluyveromyces lactis NRRL Y-1140	Mutation(s): 0 Gene Names: ABD1, KLLA0F10527g EC: 2.1.1.56
UniProt
Find proteins for Q6CKI0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CKI0 Go to UniProtKB: Q6CKI0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6CKI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG (Subject of Investigation/LOI) Query on SFG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.219 (Depositor), 0.217 (DCC)
R-Value Work: 0.187 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.962	α = 90
b = 54.789	β = 92.8
c = 112.933	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Nilson, D.J.

Fedorov, E.

Ghosh, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5T32GM007491
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10 OD020068