7Y6X | pdb_00007y6x

RRGSGG-AtPRT6 UBR box (P32)

PDB DOI: https://doi.org/10.2210/pdb7Y6X/pdb

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

Deposited: 2022-06-21 Released: 2023-07-05
Deposition Author(s): Kim, L., Song, H.K.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.220 (Depositor), 0.221 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural analyses of plant PRT6-UBR box for Cys-Arg/N-degron pathway and insights into the plant submergence resistance

Kim, L., Lin, C.C., Lin, T.J., Cao, Y.C., Chen, M.C., Chou, M.Y., Lin, W.H., Kim, M., Wu, J.L., Shih, M.C., Song, H.K., Ho, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 66.99 kDa
Atom Count: 4,594
Modeled Residue Count: 605
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase PRT6	A B C [auth D] D [auth E] E [auth F] A, B, C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth C]	76	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60 EC: 2.3.2.27
UniProt
Find proteins for F4KCC2 (Arabidopsis thaliana) Explore F4KCC2 Go to UniProtKB: F4KCC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4KCC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth G] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth G] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth G] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] CA [auth H] DA [auth C] EA [auth C] AA [auth H], BA [auth H], CA [auth H], DA [auth C], EA [auth C], FA [auth C], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth D], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth E], U [auth F], V [auth F], W [auth F], X [auth G], Y [auth G], Z [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.220 (Depositor), 0.221 (DCC)
R-Value Work: 0.201 (Depositor), 0.204 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.67	α = 90
b = 93.67	β = 90
c = 106.97	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Kim, L.

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	2021R1A6A1A10045235