MolNFT v1 · #98334 · protein
Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-T
4L6C · 5'(3')-deoxyribonucleotidase, mitochondrial: “Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-T”. X-ray diffraction, 3 ligands (0BT, MG, PO4), 2 pockets (best druggability 0.71).…
- PDB
- 4L6C
- Type
- protein
- Length
- 201 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'(3')-deoxyribonucleotidase, mitochondrial
- EC
- 3.1.3.-
- UniProt
- Q9NPB1
- Ligands
- 0BT, MG, PO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'(3')-deoxyribonucleotidase, mitochondrial (EC 3.1.3.-) | protein | 201 | 34% helix, 15% strand | Q9NPB1 |
Ligands and binding sites
- 0BT · 1-{2-deoxy-3,5-O-[(4-iodophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 309 | 0.71 | 0.84 | 32 | PO4, 0BT |
| 2 | 80 | 0.33 | 0.74 | 19 | GOL |
Compared structures
- 4L6C · Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the… · 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 0.97
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 4L6C · PDBe 4L6C · UniProt Q9NPB1
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