MolNFT v1 · #120086 · protein
Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120 complexed with sucrose
5GOP: “Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120 complexed with sucrose”. X-ray diffraction, 2 ligands (FRU, GLC), 12 pockets (best druggability 0.79). MolNFT v1 #120086 on GenesisL1: 3D structure, binding…
- 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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