MolNFT v1 · #12454 · protein
E. COLI alkaline phosphatase mutant (D153GD330N) complex with phosphate
1KH9: “E. COLI alkaline phosphatase mutant (D153GD330N) complex with phosphate”. X-ray diffraction, 3 ligands (ZN, MG, PO4), 5 pockets (best druggability 0.79). MolNFT v1 #12454 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KH9
- Type
- protein
- Length
- 888 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase
- EC
- 3.1.3.1
- UniProt
- P00634
- Ligands
- ZN, MG, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 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 | 444 | 32% helix, 21% strand | P00634 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.98 | 27 | empty |
| 2 | 130 | 0.44 | 0.77 | 30 | PO4 |
| 3 | 83 | 0.40 | 0.79 | 19 | MG, PO4 |
| 4 | 80 | 0.40 | 0.78 | 23 | empty |
| 5 | 79 | 0.28 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3955 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1KH9 · E. COLI alkaline phosphatase mutant (D153GD330N) complex with phosphate · 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 1KH9 · PDBe 1KH9 · UniProt P00634
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