Research workbench
Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdn) in complex with deoxyuridine 5'- monophosphate
Analyse Crystal structure of D12N variant of mouse cytosolic 5'(3')… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JAR
- Type
- protein
- Length
- 196 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'(3')-deoxyribonucleotidase
- EC
- 3.1.3.-
- UniProt
- Q9JM14
- Ligands
- UMP, MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'(3')-deoxyribonucleotidase (EC 3.1.3.-) | protein | 196 | 36% helix, 16% strand | Q9JM14 |
Ligands and binding sites
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 | 219 | 0.66 | 0.84 | 31 | UMP |
| 2 | 67 | 0.30 | 0.74 | 17 | empty |
Compared structures
- 2JAR · Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JM14 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, cytosolic type… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9JM14
- Elsewhere: RCSB PDB 2JAR · PDBe 2JAR · UniProt Q9JM14
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