MolNFT v1 · #129467 · protein
Crystal structure of autotaxin in complex with pf-8380
5OLB · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of autotaxin in complex with pf-8380”. X-ray diffraction, 11 ligands (6ZO, NAG, MAN), 12 pockets (best druggability 0.77). MolNFT v1 #129467 on GenesisL1…
- PDB
- 5OLB
- Type
- protein
- Length
- 785 residues
- Chains
- 1
- 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
- Q9R1E6
- Ligands
- 6ZO, NAG, MAN, BMA, FUC, ZN, CA, NA, K, CL, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 785 | 30% helix, 19% strand | Q9R1E6 |
Ligands and binding sites
- 6ZO · (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.77 | 0.79 | 82 | CL, PGE, 6ZO |
| 2 | 438 | 0.66 | 0.78 | 52 | empty |
| 3 | 265 | 0.58 | 0.78 | 25 | empty |
| 4 | 145 | 0.51 | 0.79 | 24 | empty |
| 5 | 78 | 0.42 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- Q9R1E6 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · 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 Q9R1E6
- Elsewhere: RCSB PDB 5OLB · PDBe 5OLB · UniProt Q9R1E6
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