Research workbench
Apo-form Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482
Analyse Apo-form Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UAM
- Type
- protein
- Length
- 564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.802
- Source
- Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 /…
- Molecule
- Putative ryanodine receptor
- UniProt
- Q8A5J2
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.802 · 5 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ryanodine receptor | protein | 93 | 47% helix, 11% strand | Q8A5J2 |
| B | Putative ryanodine receptor | protein | 96 | 46% helix, 10% strand | Q8A5J2 |
| C | Putative ryanodine receptor | protein | 92 | 49% helix, 11% strand | Q8A5J2 |
| D, F | Putative ryanodine receptor | protein | 94 | 48% helix, 11% strand | Q8A5J2 |
| E | Putative ryanodine receptor | protein | 95 | 47% helix, 11% strand | Q8A5J2 |
Ligands and binding sites
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 4 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.74 | 0.79 | 48 | CIT |
| 2 | 766 | 0.74 | 0.79 | 48 | CIT |
| 3 | 707 | 0.73 | 0.79 | 46 | CIT |
| 4 | 115 | 0.45 | 0.78 | 20 | empty |
| 5 | 100 | 0.41 | 0.77 | 14 | empty |
Interfaces
5 interfaces between chains.
- E–F · 2007 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1947 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1936 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 717 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 704 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 6UAM · Apo-form dimer of Y77A mutant putative ryanodine receptor from bacteroides… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8A5J2
- Elsewhere: RCSB PDB 6UAM · PDBe 6UAM · UniProt Q8A5J2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.