6ZHU | pdb_00006zhu

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
View more details

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
Modeled Residue Count: 4,681
Deposited Residue Count: 5,276
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-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 I [auth A] SDF format, chain K [auth E] SDF format, chain M [auth C] SDF format, chain O [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth E] MOL2 format, chain M [auth C] MOL2 format, chain O [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth E] mmCIF format, chain M [auth C] mmCIF format, chain O [auth G]	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 J [auth A] SDF format, chain L [auth E] SDF format, chain N [auth C] SDF format, chain P [auth G] MOL2 format, chain J [auth A] MOL2 format, chain L [auth E] MOL2 format, chain N [auth C] MOL2 format, chain P [auth G] mmCIF format, chain J [auth A] mmCIF format, chain L [auth E] mmCIF format, chain N [auth C] mmCIF format, chain P [auth G]	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]