MolNFT v1 · #85951 · protein
Yersinia kristensenii phytase apo form
4ARV: “Yersinia kristensenii phytase apo form”. X-ray diffraction, 3 ligands (TOE, P15, PO4), 7 pockets (best druggability 0.72). MolNFT v1 #85951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ARV
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytase
- EC
- 3.1.3.26
- UniProt
- H9TUK6
- Ligands
- TOE, P15, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phytase (EC 3.1.3.26) | protein | 409 | 42% helix, 15% strand | H9TUK6 |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · chains A
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.72 | 0.77 | 73 | empty |
| 2 | 545 | 0.66 | 0.77 | 48 | PO4, EDO |
| 3 | 510 | 0.65 | 0.77 | 45 | PO4, EDO |
| 4 | 254 | 0.50 | 0.75 | 36 | empty |
| 5 | 122 | 0.47 | 0.79 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 339 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ARV · Yersinia kristensenii phytase apo form · 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 H9TUK6
- Elsewhere: RCSB PDB 4ARV · PDBe 4ARV · UniProt H9TUK6
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