8ZG9 | pdb_00008zg9

Y-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1

PDB DOI: https://doi.org/10.2210/pdb8ZG9/pdb

Classification: LIGASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-09 Released: 2025-05-14
Deposition Author(s): Yang, W.S., Song, H.K.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 ?
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for the recognition of type-2 N-degron by PRT1 plant N-recognin

Yang, W.S., Song, H.K.

To be published.

Macromolecule Content

Total Structure Weight: 47.99 kDa
Atom Count: 3,455
Modelled Residue Count: 405
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Y-degron,E3 ubiquitin-protein ligase PRT1	A, B, C, D, E A, B, C, D, E, F	69	Arabidopsis thaliana	Mutation(s): 0 EC: 2.3.2.27
UniProt
Find proteins for Q8LBL5 (Arabidopsis thaliana) Explore Q8LBL5 Go to UniProtKB: Q8LBL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LBL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F]	G [auth A] H [auth A] J [auth B] K [auth B] M [auth C] G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 ?
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 48.254	α = 90
b = 85.737	β = 90
c = 85.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Yang, W.S.

Song, H.K.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A2C3008285
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021M3A9I4030068
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022M3A9G8082638