MolNFT v1 · #29622 · protein
Alkaline phosphatase from human placenta in complex with P- nitrophenyl-phosphonate
1ZED: “Alkaline phosphatase from human placenta in complex with P- nitrophenyl-phosphonate”. X-ray diffraction, 6 ligands (PNP, NAG, ZN), 4 pockets (best druggability 0.37). MolNFT v1 #29622 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1ZED
- Type
- protein
- Length
- 481 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase
- EC
- 3.1.3.1
- UniProt
- P05187
- Ligands
- PNP, NAG, ZN, MG, CA, PO3
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline phosphatase (EC 3.1.3.1) | protein | 481 | 33% helix, 18% strand | P05187 |
Ligands and binding sites
- PNP · Methyl-phosphonic acid mono-(4-nitro-phenyl) ester · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains A
- PO3 · Phosphite ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.37 | 0.80 | 15 | empty |
| 2 | 57 | 0.32 | 0.77 | 16 | empty |
| 3 | 59 | 0.30 | 0.75 | 15 | empty |
| 4 | 54 | 0.25 | 0.72 | 12 | PO3 |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ZED · Alkaline phosphatase from human placenta in complex with p-nitrophenyl-phosphonate · the same entry in another collection · chain A against A, TM-score 1.00
- P05187 · AlphaFold monomer V2.0 prediction for alkaline phosphatase, placental type (P05187) · 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 P05187
- Elsewhere: RCSB PDB 1ZED · PDBe 1ZED · UniProt P05187
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