MolNFT v2 · #227440 · protein
RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain
9CGP · Ryanodine receptor 1: “RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with…”. Electron microscopy at 3.34, 3 ligands (ATP, U1C, ZN), 20 pockets (best druggability 0.88). MolNFT…
- 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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