8U38 | pdb_00008u38

Structure of a bacterial multi-ubiquitin domain protein

PDB DOI: https://doi.org/10.2210/pdb8U38/pdb

Classification: PROTEIN BINDING
Organism(s): Methylobacterium brachiatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-07 Released: 2025-04-09
Deposition Author(s): Ye, Q., Gong, M., Corbett, K.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.275 (Depositor), 0.276 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Bacteria encode eukaryotic-like ubiquitination pathways that function in antiviral defense

Chambers, L.R., Ye, Q., Gong, M., Corbett, K.D.

To be published.

Macromolecule Content

Total Structure Weight: 108.76 kDa
Atom Count: 4,779
Modelled Residue Count: 594
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylobacterium brachiatum Ubl-BilA	A, B, C, D	243	Methylobacterium brachiatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	F [auth A], G [auth A], J [auth B], N [auth D], O [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	E [auth A] H [auth B] I [auth B] K [auth C] L [auth C] E [auth A], H [auth B], I [auth B], K [auth C], L [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D]