Research workbench
E. COLI alkaline phosphatase mutant (D330N) mimic of the transition states with aluminium fluoride
Analyse E. COLI alkaline phosphatase mutant (D330N) mimic of the transition states with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KH5
- 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
- AF3, ZN, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkaline phosphatase (EC 3.1.3.1) | protein | 444 | 31% helix, 21% strand | P00634 |
Ligands and binding sites
- AF3 · Aluminum fluoride · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 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 | 102 | 0.79 | 0.99 | 27 | empty |
| 2 | 93 | 0.39 | 0.76 | 24 | empty |
| 3 | 84 | 0.31 | 0.73 | 21 | AF3 |
| 4 | 82 | 0.29 | 0.73 | 20 | AF3 |
| 5 | 50 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3982 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1KH5 · E. COLI alkaline phosphatase mutant (D330N) mimic of the transition states with aluminium… · 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 1KH5 · PDBe 1KH5 · UniProt P00634
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