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Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride
Analyse Crystal structure of red kidney bean purple acid phosphatase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QFP
- Type
- protein
- Length
- 1,696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purple acid phosphatase
- EC
- 3.1.3.2
- UniProt
- O24319
- Ligands
- NAG, NA, FE, ZN, SO4, F
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Purple acid phosphatase (EC 3.1.3.2) | protein | 424 | 18% helix, 29% strand | O24319 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- NA · Sodium ion · metal · 11 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- F · Fluoride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.68 | 0.80 | 38 | empty |
| 2 | 417 | 0.66 | 0.79 | 38 | empty |
| 3 | 387 | 0.64 | 0.78 | 34 | empty |
| 4 | 404 | 0.63 | 0.77 | 34 | empty |
| 5 | 239 | 0.49 | 0.74 | 34 | SO4, F, NA |
Interfaces
2 interfaces between chains.
- C–D · 1540 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1508 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 2QFP · Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride · 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 O24319
- Elsewhere: RCSB PDB 2QFP · PDBe 2QFP · UniProt O24319
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