6ZXW

Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin

PDB DOI: https://doi.org/10.2210/pdb6ZXW/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-07-30 Released: 2020-09-23
Deposition Author(s): Graille, M., Wang, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.217
R-Value Work: 0.198
R-Value Observed: 0.199

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex

Wang, C., Tran, N.V., Jactel, V., Guerineau, V., Graille, M.

(2020) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 45.76 kDa
Atom Count: 3,187
Modelled Residue Count: 378
Deposited Residue Count: 386
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Guanine(10)-N2)-dimethyltransferase	A [auth G]	326	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_1676, XD48_1558
UniProt
Find proteins for O29011 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29011 Go to UniProtKB: O29011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O29011
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B [auth H]	60	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_0284, XD48_0149
UniProt
Find proteins for A0A117KMN5 (Archaeoglobus fulgidus) Explore A0A117KMN5 Go to UniProtKB: A0A117KMN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A117KMN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG Query on SFG Download Ideal Coordinates CCD File SDF format, chain C [auth G] MOL2 format, chain C [auth G]	C [auth G]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth G] Interactions & Density Focus chain C [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain Q [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G]	P [auth G], Q [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth G] Focus chain Q [auth G] Interactions & Density Focus chain P [auth G] Focus chain Q [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain R [auth H] MOL2 format, chain R [auth H]	R [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth H] Interactions & Density Focus chain R [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth G] SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] MOL2 format, chain D [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G]	D [auth G] E [auth G] F [auth G] G H [auth G] D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], L [auth G], M [auth G], N [auth G], O [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G]	J [auth G], K [auth G]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain J [auth G] Focus chain K [auth G]