6ZHT

Uba1-Ubc13 disulfide mediated complex

PDB DOI: https://doi.org/10.2210/pdb6ZHT/pdb

Classification: LIGASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-23 Released: 2022-01-12
Deposition Author(s): Schaefer, A., Misra, M., Schindelin, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263
R-Value Work: 0.206
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

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

Literature

ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system.

Misra, M., Schaefer, A., Kuhn, M., Pluska, L., Tessmer, I., Sommer, T., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 130.51 kDa
Atom Count: 9,430
Modelled Residue Count: 1,136
Deposited Residue Count: 1,154
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-activating enzyme E1 1	A [auth C]	1,001	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: UBA1, YKL210W EC: 6.2.1.45
UniProt
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22515 Go to UniProtKB: P22515
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22515
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 13	B	153	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: UBC13, YDR092W, YD6652.04 EC: 2.3.2.23
UniProt
Find proteins for P52490 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52490 Go to UniProtKB: P52490
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C SDF format, chain D [auth C] SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain R [auth B] MOL2 format, chain C MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain R [auth B]	C D [auth C] E [auth C] F [auth C] G [auth C] C, D [auth C], E [auth C], F [auth C], G [auth C], H [auth C], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain R [auth B] Interactions & Density Focus chain C Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C]	N [auth C], O [auth C], P [auth C], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]