MolNFT v1 · #29303 · protein
Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate
1Z4J · 5'(3')-deoxyribonucleotidase: “Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine…”. X-ray diffraction, 2 ligands (U2P, MG), 2 pockets (best druggability 0.70). MolNFT v1 #29303 on…
- PDB
- 1Z4J
- Type
- protein
- Length
- 194 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'(3')-deoxyribonucleotidase
- EC
- 3.1.3.-
- UniProt
- Q9NPB1
- Ligands
- U2P, MG
- Pockets
- 2 · best druggability 0.70
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 | 194 | 36% helix, 16% strand | Q9NPB1 |
Ligands and binding sites
- U2P · Phosphoric acid mono-[2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-3-yl] ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · 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 | 255 | 0.70 | 0.85 | 34 | U2P |
| 2 | 51 | 0.32 | 0.77 | 18 | empty |
Compared structures
- 1Z4J · Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NPB1 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, mitochondrial (Q9NPB1) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9NPB1
- Elsewhere: RCSB PDB 1Z4J · PDBe 1Z4J · UniProt Q9NPB1
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