Research workbench
Purple acid phytase from wheat isoform B2 - substrate complex
Analyse Purple acid phytase from wheat isoform B2 - substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GIZ
- Type
- protein
- Length
- 504 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purple acid phosphatase
- EC
- 3.1.3.2
- UniProt
- C4PKL0
- Ligands
- NAG, FE, PO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purple acid phosphatase (EC 3.1.3.2) | protein | 504 | 16% helix, 27% strand | C4PKL0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.99 | 23 | empty |
| 2 | 341 | 0.56 | 0.75 | 42 | PO4 |
| 3 | 54 | 0.43 | 0.83 | 21 | empty |
| 4 | 72 | 0.33 | 0.75 | 21 | PGE |
| 5 | 79 | 0.32 | 0.74 | 19 | PGE |
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6GIZ · Purple acid phytase from wheat isoform B2 - substrate complex · 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 C4PKL0
- Elsewhere: RCSB PDB 6GIZ · PDBe 6GIZ · UniProt C4PKL0
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