Research workbench
Crystal structure of escherichia COLI phytase at pH 4.5 (no ligand bound)
Analyse Crystal structure of escherichia COLI phytase at pH 4.5 (no ligand bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKL
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytase
- EC
- 3.1.3.2
- UniProt
- P07102
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytase (EC 3.1.3.2) | protein | 404 | 43% helix, 16% strand | P07102 |
| B | Phytase (EC 3.1.3.2) | protein | 402 | 43% helix, 16% strand | P07102 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.71 | 0.80 | 51 | empty |
| 2 | 398 | 0.60 | 0.76 | 44 | empty |
| 3 | 356 | 0.58 | 0.76 | 43 | empty |
| 4 | 72 | 0.48 | 0.84 | 18 | empty |
| 5 | 50 | 0.37 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1DKL · Crystal structure of escherichia COLI phytase at pH 4.5 (no ligand 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 B against A, TM-score 0.99
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 1DKL · PDBe 1DKL · UniProt P07102
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