Research workbench
Crystal structure of escherichia COLI phytase at pH 5.0 with HG2+ cation acting as an intermolecular bridge
Analyse Crystal structure of escherichia COLI phytase at pH 5.0 with HG2+ cation acting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKN
- 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
- HG
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytase (EC 3.1.3.2) | protein | 410 | 41% helix, 16% strand | P07102 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.61 | 0.77 | 38 | empty |
| 2 | 57 | 0.33 | 0.76 | 14 | empty |
| 3 | 70 | 0.31 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DKN · Crystal structure of escherichia COLI phytase at pH 5.0 with HG2+ cation acting as an… · 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 1DKN · PDBe 1DKN · UniProt P07102
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