MolNFT v1 · #165917 · protein
Closed dimer of Y77A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482
6UAG: “Closed dimer of Y77A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482”. X-ray diffraction, 3 ligands (GLC, FRU, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #165917 on GenesisL1: 3D structure…
- PDB
- 6UAG
- Type
- protein
- Length
- 568 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ryanodine receptor
- UniProt
- Q8A5J2
- Ligands
- GLC, FRU, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative ryanodine receptor | protein | 97 | 46% helix, 10% strand | Q8A5J2 |
| B, C | Putative ryanodine receptor | protein | 94 | 48% helix, 11% strand | Q8A5J2 |
| E, F | Putative ryanodine receptor | protein | 93 | 49% helix, 11% strand | Q8A5J2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.72 | 0.78 | 47 | GLC, FRU, SO4 |
| 2 | 725 | 0.71 | 0.78 | 51 | GLC, FRU, GOL |
| 3 | 706 | 0.71 | 0.78 | 45 | GLC, FRU, GOL |
| 4 | 158 | 0.47 | 0.77 | 23 | empty |
| 5 | 146 | 0.45 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2035 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2008 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1916 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 750 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 736 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 6UAG · Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron… · 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 6UAG · PDBe 6UAG · UniProt Q8A5J2
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