MolNFT v1 · #39860 · protein
Structure of human cytosolic deoxyribonucleotidase in complex with deoxyuridine, ALF4 and MG2+
2I7D · 5'(3')-deoxyribonucleotidase, cytosolic type: “Structure of human cytosolic deoxyribonucleotidase in complex with deoxyuridine, ALF4 and MG2+”. X-ray diffraction, 3 ligands (ALF, DUR, MG), 7 pockets (best druggability 0.71). MolNFT…
- PDB
- 2I7D
- Type
- protein
- Length
- 385 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
- ALF, DUR, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'(3')-deoxyribonucleotidase, cytosolic type (EC 3.1.3.-) | protein | 193 | 36% helix, 16% strand | Q8TCD5 |
| B | 5'(3')-deoxyribonucleotidase, cytosolic type (EC 3.1.3.-) | protein | 192 | 36% helix, 16% strand | Q8TCD5 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- DUR · 2'-deoxyuridine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.71 | 0.83 | 42 | MG, ALF, DUR |
| 2 | 349 | 0.70 | 0.82 | 36 | MG, ALF, DUR |
| 3 | 84 | 0.35 | 0.75 | 16 | empty |
| 4 | 84 | 0.32 | 0.73 | 16 | empty |
| 5 | 55 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2I7D · Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TCD5 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, cytosolic type… · a predicted model of the same protein · chain B 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 2I7D · PDBe 2I7D · UniProt Q8TCD5
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