Research workbench
Crystal structure of red kidney bean purple acid phosphatase in complex with maybridge fragment CC24201
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
- 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
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