9QDX | pdb_00009qdx

GID4 in complex with Compound 1

PDB DOI: https://doi.org/10.2210/pdb9QDX/pdb

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

Deposited: 2025-03-07 Released: 2026-03-18
Deposition Author(s): Wisniewski, J., Gorecka-Minakowska, K.M., Klejnot, M., Pastok, M.W., Skowron, A.N., Walczak, M.J.
Funding Organization(s): National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.296 (Depositor), 0.288 (DCC)
R-Value Work:
0.212 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel chemical probes and conformational flexibility of GID4 - a substrate receptor of the Human CTLH E3 ligase complex

Wisniewski, J., Gorecka-Minakowska, K.M., Klejnot, M., Pastok, M.W., Skowron, A.N., Walczak, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 19.75 kDa
Atom Count: 1,383
Modeled Residue Count: 161
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-induced degradation protein 4 homolog	A	166	Escherichia coli	Mutation(s): 0 Gene Names: GID4, C17orf39, VID24
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVV7 (Homo sapiens) Explore Q8IVV7 Go to UniProtKB: Q8IVV7
PHAROS: Q8IVV7 GTEx: ENSG00000141034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IVV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I6C (Subject of Investigation/LOI) Query on A1I6C Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{N}'-phenylpiperidine-1-carboximidamide C₁₂ H₁₇ N₃ TZEFIKHIRATNEI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.296 (Depositor), 0.288 (DCC)
R-Value Work: 0.212 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.107	α = 90
b = 40.568	β = 107.94
c = 51.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Gorecka-Minakowska, K.M.

Funding Organization	Location	Grant Number
National Center for Research and Development (Poland)	Poland	POIR.01.01.01-00-0931/19

Revision History (Full details and data files)

Version 1.0: 2026-03-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.