MolNFT v1 · #89560 · protein
Crystal structure of red kidney bean purple acid phosphatase in complex with maybridge fragment CC24201
4DSY: “Crystal structure of red kidney bean purple acid phosphatase in complex with maybridge fragment CC24201”. X-ray diffraction, 6 ligands (0LO, NAG, FUC), 19 pockets (best druggability 0.67). MolNFT v1 #89560 on GenesisL1: 3D…
- PDB
- 4DSY
- Type
- protein
- Length
- 1,700 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
- 0LO, NAG, FUC, ZN, FE, SO4
- Pockets
- 19 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purple acid phosphatase (EC 3.1.3.2) | protein | 425 | 18% helix, 29% strand | O24319 |
| B, D | Purple acid phosphatase (EC 3.1.3.2) | protein | 426 | 18% helix, 30% strand | O24319 |
| C | Purple acid phosphatase (EC 3.1.3.2) | protein | 423 | 18% helix, 30% strand | O24319 |
Ligands and binding sites
- 0LO · 5-phenylpyridine-3-carboxylic acid · ligand · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.67 | 0.79 | 42 | empty |
| 2 | 417 | 0.66 | 0.79 | 42 | GOL, SO4 |
| 3 | 403 | 0.65 | 0.78 | 32 | empty |
| 4 | 393 | 0.65 | 0.78 | 34 | empty |
| 5 | 160 | 0.42 | 0.74 | 24 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 1550 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1531 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DSY · Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge… · 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 4DSY · PDBe 4DSY · UniProt O24319
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.