Research workbench
Structure of E.COLI alkaline phosphatase mutant in complex with a phosphorylated peptide
Analyse Structure of E.COLI alkaline phosphatase mutant in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DPC
- Type
- protein
- Length
- 907 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase; Phosphorylated peptide
- EC
- 3.1.3.1
- UniProt
- P00634
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline phosphatase (EC 3.1.3.1) | protein | 449 | 29% helix, 21% strand | P00634 |
| B | Alkaline phosphatase (EC 3.1.3.1) | protein | 448 | 29% helix, 21% strand | P00634 |
| C | Phosphorylated peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.78 | 0.98 | 27 | empty |
| 2 | 116 | 0.65 | 0.89 | 32 | empty |
| 3 | 250 | 0.57 | 0.78 | 33 | PO4 |
| 4 | 250 | 0.55 | 0.77 | 25 | empty |
| 5 | 200 | 0.52 | 0.78 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3730 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 3DPC · Structure of E.coli Alkaline Phosphatase Mutant in Complex with a Phosphorylated Peptide · 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 B against A, TM-score 0.98
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 3DPC · PDBe 3DPC · UniProt P00634
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