Research workbench
The crystal structure of OCTADECYLOXY(NAPHTHALEN-1-YL)METHYLPHOSPHONIC acid in complex with red kidney bean purple acid phosphatase
Analyse The crystal structure of OCTADECYLOXY(NAPHTHALEN-1-YL)METHYLPHOSPHONIC acid in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFD
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FE(3+)-ZN(2+) purple acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P80366
- Ligands
- MF1, NAG, FUC, BMA, MAN, NA, ZN, FE, SO4, CL
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 426 | 18% helix, 29% strand | P80366 |
| B | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 425 | 18% helix, 29% strand | P80366 |
| D | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 424 | 18% helix, 29% strand | P80366 |
| C | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 423 | 18% helix, 30% strand | P80366 |
Ligands and binding sites
- MF1 · [(S)-(naphthalen-1-yl)(octadecyloxy)methyl]phosphonic acid · ligand · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains D, C
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- NA · Sodium ion · metal · 5 copies · chains A, D, C, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, C
- FE · Fe (III) ion · metal · 4 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 19 copies · chains A, D, B, C
- CL · Chloride ion · ion · chains A, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C
- PGE · Triethylene glycol · additive · 3 copies · chains A, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.68 | 0.80 | 40 | SO4, EDO |
| 2 | 449 | 0.68 | 0.80 | 39 | SO4, NA |
| 3 | 419 | 0.66 | 0.78 | 35 | empty |
| 4 | 392 | 0.65 | 0.78 | 34 | empty |
| 5 | 182 | 0.44 | 0.74 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1514 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1496 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 499 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OFD · The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosphonic acid in complex… · the same entry in another collection · chain C against C, TM-score 1.00
- P80366 · AlphaFold monomer V2.0 prediction for FE(3+)-ZN(2+) purple acid phosphatase (P80366) · a predicted model of the same protein · chain D 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 P80366
- Elsewhere: RCSB PDB 6OFD · PDBe 6OFD · UniProt P80366
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