8HMG | pdb_00008hmg

The open state of RGLG2-VWA

PDB DOI: https://doi.org/10.2210/pdb8HMG/pdb

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

Deposited: 2022-12-03 Released: 2023-12-06
Deposition Author(s): Wang, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.208 (Depositor), 0.213 (DCC)
R-Value Work:
0.183 (Depositor), 0.194 (DCC)
R-Value Observed:
0.185 (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

Ca2+-based Allosteric Switches and Shape Shifting in RGLG1 VWA domain

Wang, Q.

To be published.

Macromolecule Content

Total Structure Weight: 309.67 kDa
Atom Count: 21,046
Modeled Residue Count: 2,598
Deposited Residue Count: 2,763
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 RGLG2	A, B, C, D, E A, B, C, D, E, F, G, H, I	307	Arabidopsis thaliana	Mutation(s): 0 Gene Names: RGLG2, At5g14420, F18O22.210 EC: 2.3.2.27
UniProt
Find proteins for Q9LY87 (Arabidopsis thaliana) Explore Q9LY87 Go to UniProtKB: Q9LY87
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LY87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain EB [auth H] SDF format, chain FB [auth H] SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain KB [auth I] SDF format, chain LB [auth I] SDF format, chain MB [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain Z [auth C] SDF format, chain ZA [auth G] SDF format, chain U [auth B] SDF format, chain IA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain EB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain MB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain IA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain EB [auth H] mmCIF format, chain FB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KB [auth I] mmCIF format, chain LB [auth I] mmCIF format, chain MB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain IA [auth D]	AA [auth C] BA [auth C] CA [auth C] EB [auth H] FB [auth H] AA [auth C], BA [auth C], CA [auth C], EB [auth H], FB [auth H], HA [auth D], IA [auth D], JA [auth D], KB [auth I], LB [auth I], MB [auth I], N [auth A], O [auth A], OA [auth E], PA [auth E], T [auth B], U [auth B], UA [auth F], Z [auth C], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth F] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth F] Focus chain Z [auth C] Focus chain ZA [auth G]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth H] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GB [auth I] SDF format, chain HB [auth I] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain SA [auth F] SDF format, chain P [auth B] SDF format, chain LA [auth E] SDF format, chain IB [auth I] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain SA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain LA [auth E] MOL2 format, chain IB [auth I] mmCIF format, chain AB [auth H] mmCIF format, chain BB [auth H] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GB [auth I] mmCIF format, chain HB [auth I] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain SA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain LA [auth E] mmCIF format, chain IB [auth I]	AB [auth H] BB [auth H] CB [auth H] DA [auth D] EA [auth D] AB [auth H], BB [auth H], CB [auth H], DA [auth D], EA [auth D], FA [auth D], GB [auth I], HB [auth I], IB [auth I], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], MA [auth E], P [auth B], Q [auth B], QA [auth F], R [auth B], RA [auth F], SA [auth F], V [auth C], VA [auth G], W [auth C], WA [auth G], X [auth C], XA [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain GA [auth D] SDF format, chain JB [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth E] SDF format, chain S [auth B] SDF format, chain TA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth G] MOL2 format, chain DB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain JB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G] mmCIF format, chain DB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain JB [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth G]	DB [auth H] GA [auth D] JB [auth I] M [auth A] NA [auth E] DB [auth H], GA [auth D], JB [auth I], M [auth A], NA [auth E], S [auth B], TA [auth F], Y [auth C], YA [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth H] Focus chain GA [auth D] Focus chain JB [auth I] Focus chain M [auth A] Focus chain NA [auth E] Focus chain S [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Focus chain YA [auth G] Interactions & Density Focus chain DB [auth H] Focus chain GA [auth D] Focus chain JB [auth I] Focus chain M [auth A] Focus chain NA [auth E] Focus chain S [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Focus chain YA [auth G]