MolNFT v1 · #120085 · protein
Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120 complexed with fructose
5GOO: “Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120 complexed with fructose”. X-ray diffraction, 1 ligand (FRU), 10 pockets (best druggability 0.80). MolNFT v1 #120085 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GOO
- Type
- protein
- Length
- 1,335 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
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline invertase (EC 3.2.1.26) | protein | 447 | 49% helix, 13% strand | Q8YWS9 |
| B | Alkaline invertase (EC 3.2.1.26) | protein | 443 | 49% helix, 13% strand | Q8YWS9 |
| C | Alkaline invertase (EC 3.2.1.26) | protein | 445 | 49% helix, 12% strand | Q8YWS9 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.80 | 0.96 | 30 | empty |
| 2 | 539 | 0.79 | 0.85 | 57 | empty |
| 3 | 156 | 0.77 | 0.94 | 43 | FRU, GOL |
| 4 | 117 | 0.71 | 0.92 | 29 | FRU, GOL |
| 5 | 499 | 0.69 | 0.79 | 71 | FRU, GOL |
Interfaces
2 interfaces between chains.
- B–C · 3335 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 719 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 5GOO · 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 5GOO · PDBe 5GOO · UniProt Q8YWS9
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