MolNFT v1 · #58767 · protein
Crystal structure of metal-free E. COLI alkaline phosphatase (T155V)
3BDF: “Crystal structure of metal-free E. COLI alkaline phosphatase (T155V)”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.79). MolNFT v1 #58767 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BDF
- Type
- protein
- Length
- 866 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
- SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline phosphatase (EC 3.1.3.1) | protein | 434 | 32% helix, 22% strand | P00634 |
| B | Alkaline phosphatase (EC 3.1.3.1) | protein | 432 | 32% helix, 21% strand | P00634 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 29 | empty |
| 2 | 243 | 0.52 | 0.76 | 47 | SO4 |
| 3 | 186 | 0.42 | 0.73 | 29 | SO4 |
| 4 | 67 | 0.37 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3553 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BDF · Crystal structure of metal-free E. coli alkaline phosphatase (T155V) · 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 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 3BDF · PDBe 3BDF · UniProt P00634
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