MolNFT v1 · #122259 · protein
Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog
5IJS · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog”. X-ray diffraction, 6 ligands (5JK, NAG, ZN), 12 pockets (best…
- PDB
- 5IJS
- Type
- protein
- Length
- 784 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
- Q64610
- Ligands
- 5JK, NAG, ZN, NA, CA, IOD
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 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 | 784 | 29% helix, 19% strand | Q64610 |
Ligands and binding sites
- 5JK · 7alpha-hydroxycholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 6 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.75 | 0.81 | 52 | 5JK |
| 2 | 299 | 0.61 | 0.79 | 30 | empty |
| 3 | 228 | 0.58 | 0.79 | 39 | IOD |
| 4 | 217 | 0.55 | 0.78 | 29 | empty |
| 5 | 180 | 0.52 | 0.78 | 32 | empty |
Modifications
Observed in the structure: 14 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 5IJS · Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal… · 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 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 Q64610
- Elsewhere: RCSB PDB 5IJS · PDBe 5IJS · UniProt Q64610
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