MolNFT v1 · #120088 · protein
Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120
5GOR: “Crystal structure of alkaline invertase inva from anabaena sp. pcc 7120”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #120088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GOR
- Type
- protein
- Length
- 2,740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline invertase
- EC
- 3.2.1.26
- UniProt
- Q8YWS9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline invertase (EC 3.2.1.26) | protein | 457 | 47% helix, 12% strand | Q8YWS9 |
| B, C, E, F | Alkaline invertase (EC 3.2.1.26) | protein | 457 | 44% helix, 12% strand | Q8YWS9 |
| D | Alkaline invertase (EC 3.2.1.26) | protein | 455 | 47% helix, 12% strand | Q8YWS9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.81 | 0.89 | 55 | empty |
| 2 | 189 | 0.81 | 0.96 | 30 | empty |
| 3 | 468 | 0.81 | 0.88 | 53 | empty |
| 4 | 475 | 0.80 | 0.88 | 54 | empty |
| 5 | 151 | 0.80 | 0.96 | 29 | empty |
Interfaces
10 interfaces between chains.
- E–F · 3330 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 3319 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 3307 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5GOR · Crystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120 · 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 5GOR · PDBe 5GOR · UniProt Q8YWS9
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