MolNFT v1 · #125645 · protein
Human nucleoside diphosphate-linked moiety X motif 17 (NUDT17)
5LF8: “Human nucleoside diphosphate-linked moiety X motif 17 (NUDT17)”. X-ray diffraction, 2 ligands (EMC, PO4), 3 pockets (best druggability 0.72). MolNFT v1 #125645 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LF8
- Type
- protein
- Length
- 253 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate-linked moiety X motif 17
- EC
- 3.6.1.-
- UniProt
- P0C025
- Ligands
- EMC, PO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate-linked moiety X motif 17 (EC 3.6.1.-) | protein | 253 | 23% helix, 34% strand | P0C025 |
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 | 400 | 0.72 | 0.83 | 46 | PO4 |
| 2 | 52 | 0.36 | 0.79 | 14 | EMC |
| 3 | 61 | 0.33 | 0.76 | 17 | empty |
Compared structures
- 5LF8 · Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17) · the same entry in another collection · chain A against A, TM-score 1.00
- P0C025 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate-linked moiety X motif 17… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0C025
- Elsewhere: RCSB PDB 5LF8 · PDBe 5LF8 · UniProt P0C025
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