Research workbench
Crystal structure of zinc-deficient wild-type E. COLI alkaline phosphatase
Analyse Crystal structure of zinc-deficient wild-type E. COLI alkaline phosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BDH
- Type
- protein
- Length
- 898 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
- MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkaline phosphatase (EC 3.1.3.1) | protein | 449 | 30% helix, 21% strand | P00634 |
Ligands and binding sites
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.78 | 0.99 | 28 | empty |
| 2 | 234 | 0.56 | 0.79 | 42 | MG |
| 3 | 179 | 0.50 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3976 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BDH · Crystal structure of zinc-deficient wild-type E. coli alkaline phosphatase · 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 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 P00634
- Elsewhere: RCSB PDB 3BDH · PDBe 3BDH · UniProt P00634
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