MolNFT v1 · #166110 · protein
Open dimer of Y77A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482
6UG4: “Open dimer of Y77A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482”. X-ray diffraction, 3 ligands (CFF, PYR, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #166110 on GenesisL1: 3D structure…
- PDB
- 6UG4
- Type
- protein
- Length
- 563 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ryanodine receptor
- UniProt
- Q8A5J2
- Ligands
- CFF, PYR, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Putative ryanodine receptor | protein | 94 | 48% helix, 11% strand | Q8A5J2 |
| C | Putative ryanodine receptor | protein | 93 | 48% helix, 9% strand | Q8A5J2 |
| D | Putative ryanodine receptor | protein | 95 | 46% helix, 11% strand | Q8A5J2 |
| F | Putative ryanodine receptor | protein | 93 | 48% helix, 11% strand | Q8A5J2 |
Ligands and binding sites
- CFF · Caffeine · ligand · 9 copies · chains A, B, C, D, E, F
- PYR · Pyruvic acid · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.80 | 0.83 | 59 | CFF, GOL |
| 2 | 1091 | 0.79 | 0.81 | 89 | SO4, CFF, GOL, PYR |
| 3 | 836 | 0.78 | 0.81 | 67 | CFF, GOL |
| 4 | 158 | 0.45 | 0.76 | 19 | empty |
| 5 | 146 | 0.43 | 0.76 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2172 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2115 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2052 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 717 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 6UG4 · Open 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 6UG4 · PDBe 6UG4 · UniProt Q8A5J2
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