6ZHU

Yeast Uba1 in complex with Ubc3 and ATP

PDB DOI: https://doi.org/10.2210/pdb6ZHU/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.263
R-Value Work: 0.217
R-Value Observed: 0.219

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 596.1 kDa
Atom Count: 37,219
Modelled Residue Count: 4,681
Deposited Residue Count: 5,276
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2-34 kDa	A [auth B], B [auth F], C [auth D], D [auth H]	295	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C EC: 2.3.2.23
UniProt
Find proteins for P14682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14682 Go to UniProtKB: P14682
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14682
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-activating enzyme E1 1	E [auth A], F [auth E], G [auth C], H [auth G]	1,024	Saccharomyces cerevisiae	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain M [auth C] SDF format, chain O [auth G] SDF format, chain I [auth A] MOL2 format, chain K [auth E] MOL2 format, chain M [auth C] MOL2 format, chain O [auth G] MOL2 format, chain I [auth A] mmCIF format, chain K [auth E] mmCIF format, chain M [auth C] mmCIF format, chain O [auth G] mmCIF format, chain I [auth A]	I [auth A], K [auth E], M [auth C], O [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth E] Focus chain M [auth C] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth E] Focus chain M [auth C] Focus chain O [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain N [auth C] SDF format, chain P [auth G] SDF format, chain J [auth A] MOL2 format, chain L [auth E] MOL2 format, chain N [auth C] MOL2 format, chain P [auth G] MOL2 format, chain J [auth A] mmCIF format, chain L [auth E] mmCIF format, chain N [auth C] mmCIF format, chain P [auth G] mmCIF format, chain J [auth A]	J [auth A], L [auth E], N [auth C], P [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth E] Focus chain N [auth C] Focus chain P [auth G] Interactions & Density Focus chain J [auth A] Focus chain L [auth E] Focus chain N [auth C] Focus chain P [auth G]