Research workbench
Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
Analyse Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KX3
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic 5'-nucleotidase 3
- EC
- 3.1.3.5
- UniProt
- Q9D020
- Ligands
- DT, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic 5'-nucleotidase 3 (EC 3.1.3.5) | protein | 291 | 47% helix, 19% strand | Q9D020 |
Ligands and binding sites
- DT · Thymidine-5'-monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.80 | 0.90 | 61 | DT, MG, EDO |
| 2 | 64 | 0.31 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4KX3 · Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D020 · AlphaFold monomer V2.0 prediction for cytosolic 5'-nucleotidase 3A (Q9D020) · 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 Q9D020
- Elsewhere: RCSB PDB 4KX3 · PDBe 4KX3 · UniProt Q9D020
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.