MolNFT v1 · #84416 · protein
Structure of purple acid phosphatase PPD1 isolated from yellow lupin (lupinus luteus) seeds
3ZK4 · Diphosphonucleotide phosphatase 1: “Structure of purple acid phosphatase PPD1 isolated from yellow lupin (lupinus luteus) seeds”. X-ray diffraction, 5 ligands (NAG, FUC, FE), 20 pockets (best druggability 0.82). MolNFT v1 #84416 on…
- 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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