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Crystal structure of ectonucleotide PHOSPHODIESTERASE/PYROPHOSPHATASE- 3 (NPP3) in complex with udpglcnac
Analyse Crystal structure of ectonucleotide PHOSPHODIESTERASE/PYROPHOSPHATASE- 3 (NPP3)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F30
- Type
- protein
- Length
- 1,443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 3
- EC
- 3.1.4.1, 3.6.1.9
- UniProt
- P97675
- Ligands
- UD1, NAG, BMA, ZN, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 3 (EC 3.1.4.1, 3.6.1.9) | protein | 721 | 29% helix, 20% strand | P97675 |
| B | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 3 (EC 3.1.4.1, 3.6.1.9) | protein | 722 | 28% helix, 20% strand | P97675 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.69 | 0.79 | 71 | empty |
| 2 | 347 | 0.64 | 0.79 | 45 | empty |
| 3 | 139 | 0.57 | 0.83 | 24 | empty |
| 4 | 115 | 0.56 | 0.84 | 25 | empty |
| 5 | 275 | 0.56 | 0.77 | 40 | UD1 |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6F30 · Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- P97675 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P97675
- Elsewhere: RCSB PDB 6F30 · PDBe 6F30 · UniProt P97675
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