Research workbench
High resolutin structure of human cytosolic 5'(3')- deoxyribonucleotidase
Analyse High resolutin structure of human cytosolic 5'(3')- deoxyribonucleotidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L57
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'(3')-deoxyribonucleotidase, cytosolic type
- EC
- 3.1.3.-
- UniProt
- Q8TCD5
- Ligands
- MG, NA, PO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'(3')-deoxyribonucleotidase, cytosolic type (EC 3.1.3.-) | protein | 192 | 36% helix, 15% strand | Q8TCD5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.72 | 0.76 | 65 | empty |
| 2 | 285 | 0.70 | 0.84 | 34 | MG, PO4, GOL |
| 3 | 307 | 0.68 | 0.82 | 33 | MG, PO4, GOL |
| 4 | 52 | 0.29 | 0.76 | 13 | empty |
| 5 | 53 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 244 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4L57 · High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase · the same entry in another collection · chain B against B, TM-score 1.00
- Q8TCD5 · 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 Q8TCD5
- Elsewhere: RCSB PDB 4L57 · PDBe 4L57 · UniProt Q8TCD5
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