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Crystal structure of a nucleoside triphosphate diphosphohydrolase (ntpdase) from the legume vigna unguiculata subsp. cylindrica (dolichos biflorus) in complex with phosphate and manganese
Analyse Crystal structure of a nucleoside triphosphate diphosphohydrolase (ntpdase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7X
- Type
- protein
- Length
- 412 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nod factor binding lectin-nucleotide phosphohydrolase
- UniProt
- Q9XFC9
- Ligands
- MN, PO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Nod factor binding lectin-nucleotide phosphohydrolase | protein | 412 | 36% helix, 26% strand | Q9XFC9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.74 | 0.83 | 67 | PO4, MN |
| 2 | 78 | 0.37 | 0.77 | 17 | empty |
| 3 | 57 | 0.34 | 0.77 | 10 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5U7X · Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the… · the same entry in another collection · chain F against F, 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 Q9XFC9
- Elsewhere: RCSB PDB 5U7X · PDBe 5U7X · UniProt Q9XFC9
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