Research workbench
Structure of purple acid phosphatase PPD1 isolated from yellow lupin (lupinus luteus) seeds
Analyse Structure of purple acid phosphatase PPD1 isolated from yellow lupin (lupinus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZK4
- Type
- protein
- Length
- 1,708 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphonucleotide phosphatase 1
- EC
- 3.1.3.2
- UniProt
- Q8VX11
- Ligands
- NAG, FUC, FE, MN, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphonucleotide phosphatase 1 (EC 3.1.3.2) | protein | 569 | 13% helix, 34% strand | Q8VX11 |
| B | Diphosphonucleotide phosphatase 1 (EC 3.1.3.2) | protein | 571 | 13% helix, 34% strand | Q8VX11 |
| C | Diphosphonucleotide phosphatase 1 (EC 3.1.3.2) | protein | 568 | 14% helix, 34% strand | Q8VX11 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.82 | 0.83 | 134 | empty |
| 2 | 327 | 0.76 | 0.88 | 32 | empty |
| 3 | 324 | 0.76 | 0.87 | 30 | empty |
| 4 | 334 | 0.75 | 0.87 | 30 | empty |
| 5 | 153 | 0.57 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1660 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1640 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1627 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 3ZK4 · Structure of purple acid phosphatase PPD1 isolated from yellow lupin (Lupinus luteus)… · 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 Q8VX11
- Elsewhere: RCSB PDB 3ZK4 · PDBe 3ZK4 · UniProt Q8VX11
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