MolNFT v1 · #121318 · protein + DNA
Crystal structure of mouse autotaxin in complex with a DNA aptamer
5HRT · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of mouse autotaxin in complex with a DNA aptamer”. X-ray diffraction, 8 ligands (MAN, NAG, BMA), 15 pockets (best druggability 0.84). MolNFT v1 #121318 on…
- PDB
- 5HRT
- Type
- protein + DNA
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2; Modified DNA (34-mer)
- EC
- 3.1.4.39
- UniProt
- Q9R1E6
- Ligands
- MAN, NAG, BMA, ZN, CA, NA, K, CL
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 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 | 786 | 30% helix, 19% strand | Q9R1E6 |
| B | Modified DNA (34-mer) | dna | 34 | — | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.84 | 0.85 | 79 | CL, GOL |
| 2 | 328 | 0.61 | 0.78 | 34 | GOL |
| 3 | 296 | 0.60 | 0.78 | 44 | empty |
| 4 | 231 | 0.53 | 0.76 | 40 | empty |
| 5 | 93 | 0.45 | 0.79 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1157 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 15 disulfide, 9 modified, 2 glycan (disulfide, nucleotide modification, N-glycosylation).
Compared structures
- 5HRT · Crystal structure of mouse autotaxin in complex with a DNA aptamer · the same entry in another collection · chain A against A, TM-score 1.00
- 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 5HRT · PDBe 5HRT · UniProt Q9R1E6
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