Research workbench
Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pmcp-U
Analyse Crystal structure of human mitochondrial deoxyribonucleotidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q92
- Type
- protein
- Length
- 195 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5(3)-deoxyribonucleotidase
- EC
- 3.1.3.5
- UniProt
- Q9NPB1
- Ligands
- DRM, MG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5(3)-deoxyribonucleotidase (EC 3.1.3.5) | protein | 195 | 34% helix, 15% strand | Q9NPB1 |
Ligands and binding sites
- DRM · {[(1R,2S)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}methylphosphonic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 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 | 337 | 0.72 | 0.84 | 44 | DRM |
Compared structures
- 1Q92 · 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 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 1Q92 · PDBe 1Q92 · UniProt Q9NPB1
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