13SB | pdb_000013sb

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1456069604

PDB DOI: https://doi.org/10.2210/pdb13SB/pdb
Deposition Group: G_1002355 (changed state) ExploreG_1002355

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-10 Released: 2025-12-10
Deposition Author(s): Bradshaw, W.J., Guenther, F., Murphy, E.J.
Funding Organization(s): Alzheimers Research UK (ARUK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.218 (Depositor), 0.214 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition

Bradshaw, W.J., Guenther, F., Murphy, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 36.29 kDa
Atom Count: 2,734
Modeled Residue Count: 283
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase MYLIP	A, B, C, D	78	Homo sapiens	Mutation(s): 0 Gene Names: MYLIP, BZF1, IDOL, BM-023, PP5242 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WY64 (Homo sapiens) Explore Q8WY64 Go to UniProtKB: Q8WY64
PHAROS: Q8WY64 GTEx: ENSG00000007944
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WY64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KF8 (Subject of Investigation/LOI) Query on KF8 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D]	I [auth B], O [auth D]	N-[(3S)-piperidin-3-yl]benzamide C₁₂ H₁₆ N₂ O ZFLKDMGBVZHBAC-NSHDSACASA-N		Interactions Focus chain I [auth B] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain O [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth C] E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]