MolNFT v1 · #49164 · protein
Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride
2QFP: “Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride”. X-ray diffraction, 6 ligands (NAG, NA, FE), 15 pockets (best druggability 0.68). MolNFT v1 #49164 on GenesisL1: 3D structure, binding sites and…
- 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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