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Crystal structure of sucrose 6F-phosphate phosphorylase from thermoanaerobacter thermosaccharolyticum
Analyse Crystal structure of sucrose 6F-phosphate phosphorylase from thermoanaerobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9V
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose 6(F)-phosphate phosphorylase
- EC
- 2.4.1.329
- UniProt
- D9TT09
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sucrose 6(F)-phosphate phosphorylase (EC 2.4.1.329) | protein | 490 | 37% helix, 20% strand | D9TT09 |
| B | Sucrose 6(F)-phosphate phosphorylase (EC 2.4.1.329) | protein | 492 | 37% helix, 20% strand | D9TT09 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.79 | 0.85 | 73 | BTB, SO4, P6G |
| 2 | 251 | 0.77 | 0.91 | 41 | BTB, SO4 |
| 3 | 419 | 0.71 | 0.82 | 36 | SO4 |
| 4 | 444 | 0.69 | 0.80 | 37 | empty |
| 5 | 116 | 0.45 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6S9V · Crystal structure of sucrose 6F-phosphate phosphorylase from Thermoanaerobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- D9TT09 · AlphaFold monomer V2.0 prediction for sucrose 6(F)-phosphate phosphorylase (D9TT09) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 D9TT09
- Elsewhere: RCSB PDB 6S9V · PDBe 6S9V · UniProt D9TT09
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