Research workbench
RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain
Analyse RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9CGP
- Type
- protein
- Length
- 17,460 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.34
- Source
- Homo sapiens; Oryctolagus cuniculus
- Molecule
- Ryanodine receptor 1; Peptidyl-prolyl cis-trans isomerase FKBP1B
- EC
- 5.2.1.8
- UniProt
- P11716, P68106
- Ligands
- ATP, U1C, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.34 · 2 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ryanodine receptor 1 | protein | 4258 | 46% helix, 9% strand | P11716 |
| E, F, G, H | Peptidyl-prolyl cis-trans isomerase FKBP1B (EC 5.2.1.8) | protein | 107 | 14% helix, 24% strand | P68106 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- U1C · Dantrolene · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc 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 | 847 | 0.88 | 0.90 | 113 | empty |
| 2 | 832 | 0.88 | 0.90 | 118 | empty |
| 3 | 1031 | 0.88 | 0.88 | 109 | empty |
| 4 | 1076 | 0.87 | 0.88 | 112 | empty |
| 5 | 1098 | 0.87 | 0.88 | 133 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3480 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3479 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 3467 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3466 Ų buried · 20 hydrogen bonds · protein-protein
- C–G · 1534 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- P68106 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1B (P68106) · a predicted model of the same protein · chain H against A, TM-score 0.95
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 P11716
- Every structure of UniProt P68106
- Elsewhere: RCSB PDB 9CGP · PDBe 9CGP · UniProt P11716 · UniProt P68106
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