MolNFT v1 · #125147 · protein
Crystal structure of autotaxin and compound 1
5L0E · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of autotaxin and compound 1”. X-ray diffraction, 6 ligands (6ZN, MAN, NAG), 20 pockets (best druggability 0.75). MolNFT v1 #125147 on GenesisL1: 3D…
- PDB
- 5L0E
- Type
- protein
- Length
- 1,565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2
- EC
- 3.1.4.39
- UniProt
- Q64610
- Ligands
- 6ZN, MAN, NAG, BMA, ZN, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 783 | 29% helix, 20% strand | Q64610 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 782 | 29% helix, 19% strand | Q64610 |
Ligands and binding sites
- 6ZN · 6-(3-{2-[(2,3-dihydro-1H-inden-2-yl)amino]-7,8-dihydropyrido[4,3-d]pyrimidin-6(5H)-yl}propanoyl)-1,3-benzoxazol-2(3H)-one · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.75 | 0.78 | 96 | 6ZN, CL, ZN |
| 2 | 741 | 0.75 | 0.80 | 63 | 6ZN, CL |
| 3 | 443 | 0.67 | 0.79 | 46 | empty |
| 4 | 288 | 0.60 | 0.79 | 29 | empty |
| 5 | 303 | 0.60 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 153 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 Q64610
- Elsewhere: RCSB PDB 5L0E · PDBe 5L0E · UniProt Q64610
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