9EWP

Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain

PDB DOI: https://doi.org/10.2210/pdb9EWP/pdb

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

Deposited: 2024-04-04 Released: 2024-11-20
Deposition Author(s): Swarnkar, A., Stein, A.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.156
R-Value Work: 0.135
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

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

Literature

Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes

Swarnkar, A., Leidner, F., Rout, A.K., Ainatzi, S., Schmidt, C.C., Becker, S., Urlaub, H., Griesinger, C., Grubmuller, H., Stein, A.

(2024) EMBO J

DOI: https://doi.org/10.1038/s44318-024-00301-3

Macromolecule Content

Total Structure Weight: 21.14 kDa
Atom Count: 1,662
Modelled Residue Count: 172
Deposited Residue Count: 178
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 6	A	178	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: UBC6, GI527_G0001907 EC: 2.3.2.23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A]	K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]