8OUM

Arf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP

PDB DOI: https://doi.org/10.2210/pdb8OUM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Promethearchaeati archaeon
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-24 Released: 2024-05-01
Deposition Author(s): Menetrey, J., Jackson, C., Dacks, J.B., Elias, M., Vargova, R.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.267
R-Value Work: 0.236
R-Value Observed: 0.238

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

Ligand Structure Quality Assessment

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

Literature

Arf Family GTPases are present in Asgard archaea

Menetrey, J.

To be published.

Macromolecule Content

Total Structure Weight: 103.69 kDa
Atom Count: 6,737
Modelled Residue Count: 851
Deposited Residue Count: 890
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A, B, C, D, E	178	Promethearchaeati archaeon	Mutation(s): 1 Gene Names: FK733_07565
UniProt
Find proteins for A0A8J7ZFD1 (Asgard group archaeon) Explore A0A8J7ZFD1 Go to UniProtKB: A0A8J7ZFD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8J7ZFD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E]	F [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]