Research workbench
Crystal structure of mouse ENPP1 in complex with tmp
Analyse Crystal structure of mouse ENPP1 in complex with tmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GTX
- Type
- protein
- Length
- 1,403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2, alkaline…
- EC
- 3.1.4.39
- UniProt
- Q9R1E6, G3X9S2
- Ligands
- TMP, NAG, MAN, BMA, ZN, CA
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2, alkaline phosphodiesterase I (EC 3.1.4.39) | protein | 706 | 27% helix, 21% strand | Q9R1E6, G3X9S2 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2, alkaline phosphodiesterase I (EC 3.1.4.39) | protein | 697 | 27% helix, 21% strand | Q9R1E6, G3X9S2 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.84 | 0.85 | 116 | empty |
| 2 | 485 | 0.64 | 0.76 | 62 | empty |
| 3 | 71 | 0.62 | 0.90 | 20 | empty |
| 4 | 75 | 0.61 | 0.90 | 19 | empty |
| 5 | 98 | 0.58 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4GTX · Crystal structure of mouse Enpp1 in complex with TMP · 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 B against A, TM-score 0.94
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
- Every structure of UniProt G3X9S2
- Elsewhere: RCSB PDB 4GTX · PDBe 4GTX · UniProt Q9R1E6 · UniProt G3X9S2
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