Research workbench
Crystal structure of spap: an novel alkaline phosphatase from bacterium sphingomonas sp. strain bsar-1
Analyse Crystal structure of spap: an novel alkaline phosphatase from bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q3Q
- Type
- protein
- Length
- 526 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase
- EC
- 3.1.3.1
- UniProt
- A1YYW7
- Ligands
- KOP, ZN, CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline phosphatase (EC 3.1.3.1) | protein | 526 | 36% helix, 17% strand | A1YYW7 |
Ligands and binding sites
- KOP · methyl dihydrogen phosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.70 | 0.80 | 86 | ZN, GOL, KOP |
| 2 | 54 | 0.30 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3Q3Q · Crystal Structure of SPAP: an novel alkaline phosphatase from bacterium Sphingomonas sp.… · the same entry in another collection · chain A against A, TM-score 1.00
- A1YYW7 · AlphaFold monomer V2.0 prediction for alkaline phosphatase phok (A1YYW7) · 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 A1YYW7
- Elsewhere: RCSB PDB 3Q3Q · PDBe 3Q3Q · UniProt A1YYW7
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