MolNFT v1 · #125153 · protein
Crystal structure of autotaxin and compound pf-8380
5L0K · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of autotaxin and compound pf-8380”. X-ray diffraction, 6 ligands (6ZO, NAG, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #125153 on GenesisL1: 3D…
- PDB
- 5L0K
- Type
- protein
- Length
- 1,554 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
- 6ZO, NAG, BMA, ZN, CA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 777 | 28% helix, 19% strand | Q64610 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 777 | 27% helix, 18% strand | Q64610 |
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 · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.82 | 0.83 | 140 | 6ZO, CL |
| 2 | 679 | 0.75 | 0.80 | 81 | 6ZO, CL |
| 3 | 304 | 0.64 | 0.80 | 31 | empty |
| 4 | 266 | 0.61 | 0.80 | 37 | empty |
| 5 | 216 | 0.61 | 0.81 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5L0K · Crystal Structure of Autotaxin and Compound PF-8380 · the same entry in another collection · chain A against A, TM-score 1.00
- Q64610 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain B 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 Q64610
- Elsewhere: RCSB PDB 5L0K · PDBe 5L0K · UniProt Q64610
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