MolNFT v1 · #41022 · protein
Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdn) in complex with 3'-azidothymidine 5'- monophosphate
2JAU · 5'(3')-deoxyribonucleotidase: “Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdn) in complex with…”. X-ray diffraction, 3 ligands (ATM, MG, PO4), 1 pocket (best druggability 0.70). MolNFT v1…
- PDB
- 2JAU
- 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
- ATM, MG, PO4
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'(3')-deoxyribonucleotidase (EC 3.1.3.-) | protein | 194 | 35% helix, 16% strand | Q9NPB1 |
Ligands and binding sites
- ATM · 3'-azido-3'-deoxythymidine-5'-monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.70 | 0.83 | 47 | PO4, ATM, MG |
Compared structures
- 2JAU · Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase… · 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 2JAU · PDBe 2JAU · UniProt Q9NPB1
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