Research workbench
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-inactivated conformation class 1(Dataset-A)
Analyse Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TDJ
- Type
- protein
- Length
- 16,532 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Oryctolagus cuniculus
- Molecule
- Ryanodine receptor 1,Ryanodine receptor 1,RyR1
- UniProt
- P11716
- Ligands
- ACP, CA, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.7 · 1 distinct chain · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ryanodine receptor 1,Ryanodine receptor 1,RyR1 | protein | 4133 | 39% helix, 9% strand | P11716 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 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 | 1024 | 0.87 | 0.88 | 122 | empty |
| 2 | 1024 | 0.87 | 0.88 | 126 | empty |
| 3 | 1024 | 0.87 | 0.88 | 131 | empty |
| 4 | 1089 | 0.87 | 0.88 | 138 | empty |
| 5 | 1084 | 0.86 | 0.87 | 158 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3249 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3235 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 3232 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 3213 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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
- Elsewhere: RCSB PDB 7TDJ · PDBe 7TDJ · UniProt P11716
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