Research workbench
Structure of recombinant RyR2 (Ca2+ dataset, class 3, open state)
Analyse Structure of recombinant RyR2 (Ca2+ dataset, class 3, open state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VMQ
- Type
- protein
- Length
- 16,392 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Homo sapiens; Mus musculus
- Molecule
- Ryanodine receptor 2; Peptidyl-prolyl cis-trans isomerase FKBP1B
- EC
- 5.2.1.8
- UniProt
- E9Q401, P68106
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.7 · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ryanodine receptor 2 | protein | 3991 | 50% helix, 10% strand | E9Q401 |
| G, H, I, J | Peptidyl-prolyl cis-trans isomerase FKBP1B (EC 5.2.1.8) | protein | 107 | 10% helix, 29% strand | P68106 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.85 | 0.88 | 123 | empty |
| 2 | 994 | 0.84 | 0.85 | 136 | empty |
| 3 | 1002 | 0.84 | 0.85 | 138 | empty |
| 4 | 922 | 0.84 | 0.85 | 128 | empty |
| 5 | 1119 | 0.82 | 0.83 | 130 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3269 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 3268 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 3231 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 3163 Ų buried · 22 hydrogen bonds · protein-protein
- C–I · 1628 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- P68106 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1B (P68106) · a predicted model of the same protein · chain I against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E9Q401
- Every structure of UniProt P68106
- Elsewhere: RCSB PDB 7VMQ · PDBe 7VMQ · UniProt E9Q401 · UniProt P68106
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