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MolNFT v1 · #29620 · protein

X-ray structure of alkaline phosphatase from human placenta in complex with 5'-AMP

1ZEB: “X-ray structure of alkaline phosphatase from human placenta in complex with 5'-AMP”. X-ray diffraction, 4 ligands (NAG, ZN, MG), 3 pockets (best druggability 0.35). MolNFT v1 #29620 on GenesisL1: 3D structure, binding sites and…

PDB
1ZEB
Type
protein
Length
480 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
NAG, ZN, MG, CA
Pockets
3 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAlkaline phosphatase (EC 3.1.3.1)protein48034% helix, 17% strandP05187

Ligands and binding sites

  • 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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1700.350.7716empty
2560.310.7614empty
3550.240.7214empty

Modifications

Observed in the structure: 2 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).

Compared structures

  • 1ZEB · X-ray structure of alkaline phosphatase from human placenta in complex with 5'-AMP · 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

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