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Crystal structure of phytate complex escherichia COLI phytase at pH 5.0. phytate is bound with its 3-phosphate in the active site. HG2+ cation acts as an intermolecular bridge
Analyse Crystal structure of phytate complex escherichia COLI phytase at pH 5.0.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKQ
- Type
- protein
- Length
- 410 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytase
- EC
- 3.1.3.2
- UniProt
- P07102
- Ligands
- IHP, HG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytase (EC 3.1.3.2) | protein | 410 | 42% helix, 16% strand | P07102 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
- HG · Mercury (II) ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.62 | 0.78 | 40 | IHP |
| 2 | 60 | 0.37 | 0.79 | 16 | empty |
| 3 | 58 | 0.31 | 0.75 | 14 | empty |
| 4 | 55 | 0.29 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DKQ · Crystal structure of phytate complex escherichia COLI phytase at pH 5.0. phytate is bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P07102 · AlphaFold monomer V2.0 prediction for periplasmic appa protein (P07102) · a predicted model of the same protein · 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 P07102
- Elsewhere: RCSB PDB 1DKQ · PDBe 1DKQ · UniProt P07102
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