Research workbench
Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120 complexed with sucrose
Analyse Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GOP
- Type
- protein
- Length
- 1,318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline invertase
- EC
- 3.2.1.26
- UniProt
- Q8YWS9
- Ligands
- FRU, GLC
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline invertase (EC 3.2.1.26) | protein | 447 | 49% helix, 11% strand | Q8YWS9 |
| B | Alkaline invertase (EC 3.2.1.26) | protein | 437 | 50% helix, 13% strand | Q8YWS9 |
| C | Alkaline invertase (EC 3.2.1.26) | protein | 434 | 50% helix, 10% strand | Q8YWS9 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, C, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.79 | 0.97 | 41 | empty |
| 2 | 508 | 0.77 | 0.85 | 53 | empty |
| 3 | 125 | 0.72 | 0.92 | 32 | FRU |
| 4 | 114 | 0.70 | 0.92 | 29 | GLC, FRU |
| 5 | 238 | 0.61 | 0.81 | 30 | GLC, FRU |
Interfaces
2 interfaces between chains.
- B–C · 3059 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 5GOP · Crystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120 complexed with… · 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 Q8YWS9
- Elsewhere: RCSB PDB 5GOP · PDBe 5GOP · UniProt Q8YWS9
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