Research workbench
Structure of D153H/K328W E. coli alkaline phosphatase in presence of cobalt at 1.77 A resolution
Analyse Structure of D153H/K328W E. coli alkaline phosphatase in presence of cobalt at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y7A
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.77
- Source
- Escherichia coli
- Molecule
- Alkaline phosphatase
- EC
- 3.1.3.1
- UniProt
- P00634
- Ligands
- CO, PO4, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.77 · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkaline phosphatase (EC 3.1.3.1) | protein | 449 | 32% helix, 21% strand | P00634 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.78 | 0.99 | 25 | empty |
| 2 | 58 | 0.53 | 0.88 | 14 | empty |
| 3 | 61 | 0.52 | 0.86 | 14 | empty |
| 4 | 163 | 0.43 | 0.74 | 25 | PO4 |
| 5 | 135 | 0.40 | 0.75 | 30 | PO4 |
Interfaces
1 interface between chains.
- A–B · 3897 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1Y7A · Structure of D153H/K328W E. COLI alkaline phosphatase in presence of cobalt at 1.77 a… · the same entry in another collection · chain A against A, TM-score 1.00
- P00634 · AlphaFold monomer V2.0 prediction for alkaline phosphatase (P00634) · 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 P00634
- Elsewhere: RCSB PDB 1Y7A · PDBe 1Y7A · UniProt P00634
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