8YRE | pdb_00008yre

Crystal structure of Arabidopsis VTC1-KJC2

PDB DOI: https://doi.org/10.2210/pdb8YRE/pdb

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

Deposited: 2024-03-21 Released: 2025-04-02
Deposition Author(s): Zhang, C., Liu, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.54 Å
R-Value Free:
0.295 (Depositor), 0.294 (DCC)
R-Value Work:
0.261 (Depositor), 0.261 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural insight into the regulation of GDP-mannose pyrophosphorylase activity of Arabidopsis KJC2-VTC1 complex

Zhang, C., Liu, L.

To be published.

Macromolecule Content

Total Structure Weight: 254.99 kDa
Atom Count: 17,197
Modeled Residue Count: 2,230
Deposited Residue Count: 2,301
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-glucose pyrophosphorylase family protein	A, B, C	406	Arabidopsis thaliana	Mutation(s): 0 Gene Names: KJC2, At2g04650, F28I8.31, F28I8_31
UniProt
Find proteins for F4IFA4 (Arabidopsis thaliana) Explore F4IFA4 Go to UniProtKB: F4IFA4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4IFA4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-1-phosphate guanylyltransferase 1	D, E, F	361	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CYT1, EMB101, GMP1, HSN1, SOZ1, VTC1, At2g39770, T5I7.7 EC: 2.7.7.13
UniProt
Find proteins for O22287 (Arabidopsis thaliana) Explore O22287 Go to UniProtKB: O22287
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O22287
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain K [auth D] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain K [auth D] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain K [auth D] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth D] G [auth A], H [auth A], I [auth A], J [auth B], K [auth D], L [auth D], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]