MolNFT v1 · #159131 · protein
The crystal structure of OCTADECYLOXY(NAPHTHALEN-1-YL)METHYLPHOSPHONIC acid in complex with red kidney bean purple acid phosphatase
6OFD: “The crystal structure of OCTADECYLOXY(NAPHTHALEN-1-YL)METHYLPHOSPHONIC acid in complex with red kidney bean…”. X-ray diffraction, 10 ligands (MF1, NAG, FUC). MolNFT v1 #159131 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6OFD
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P80366
- Ligands
- MF1, NAG, FUC, BMA, MAN, NA, ZN, FE, SO4, CL
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 426 | — | P80366 |
| B | — | protein | 425 | — | P80366 |
| D | — | protein | 424 | — | P80366 |
| C | — | protein | 423 | — | P80366 |
Ligands and binding sites
- MF1 · [(S)-(naphthalen-1-yl)(octadecyloxy)methyl]phosphonic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains 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.
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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