9E1G

Structure of RyR1 in the primed state in the presence of oxypurinol

PDB DOI: https://doi.org/10.2210/pdb9E1G/pdb
EM Map EMD-47393: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2024-10-21 Released: 2024-10-30
Deposition Author(s): Miotto, M.C., Marks, A.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

Targeting Ryanodine Receptors with Allopurinol and Xanthine Derivatives for the Treatment of Cardiac and Musculoskeletal Weakness Disorders

Miotto, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 2,314.56 kDa
Atom Count: 144,104
Modelled Residue Count: 18,044
Deposited Residue Count: 20,580
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, F [auth B], G [auth D], H [auth C]	5,037	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	B [auth E], C [auth H], D [auth G], E [auth F]	108	Oryctolagus cuniculus	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for P62943 (Oryctolagus cuniculus) Explore P62943 Go to UniProtKB: P62943
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62943
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth D] MOL2 format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth D]	I [auth A], M [auth B], Q [auth D], U [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth D] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth D] Focus chain U [auth C]
141 (Subject of Investigation/LOI) Query on 141 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain T [auth D] SDF format, chain X [auth C] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth D] MOL2 format, chain X [auth C] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth D] mmCIF format, chain X [auth C]	L [auth A], P [auth B], T [auth D], X [auth C]	Oxypurinol C₅ H₄ N₄ O₂ HXNFUBHNUDHIGC-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth D] Focus chain X [auth C] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth D] Focus chain X [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain S [auth D] SDF format, chain W [auth C] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth D] MOL2 format, chain W [auth C] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth D] mmCIF format, chain W [auth C]	K [auth A], O [auth B], S [auth D], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth D] Focus chain W [auth C] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth D] Focus chain W [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain R [auth D] SDF format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth D] MOL2 format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth D] mmCIF format, chain V [auth C]	J [auth A], N [auth B], R [auth D], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain V [auth C]