Research workbench
Refinement of placental alkaline phosphatase complexed with nitrophenyl
Analyse Refinement of placental alkaline phosphatase complexed with nitrophenyl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MK0
- Type
- protein
- Length
- 481 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase, placental type
- EC
- 3.1.3.1
- UniProt
- P05187
- Ligands
- NPO, NAG, ZN, MG, CA, PO4
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline phosphatase, placental type (EC 3.1.3.1) | protein | 481 | 33% helix, 18% strand | P05187 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.35 | 0.76 | 16 | empty |
| 2 | 54 | 0.32 | 0.77 | 17 | empty |
| 3 | 63 | 0.25 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 3MK0 · Refinement of placental alkaline phosphatase complexed with nitrophenyl · 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 3MK0 · PDBe 3MK0 · UniProt P05187
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