Research workbench
Human dutpase in complex with novel uracil derivative
Analyse Human dutpase in complex with novel uracil derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ARN
- Type
- protein
- Length
- 375 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- P33316
- Ligands
- MSJ, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 125 | 6% helix, 47% strand | P33316 |
Ligands and binding sites
- MSJ · N-{5-[(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)methoxy]-2-methylpentan-2-yl}benzenesulfonamide · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.98 | 35 | MG |
| 2 | 154 | 0.46 | 0.76 | 29 | MSJ |
| 3 | 171 | 0.46 | 0.76 | 29 | MSJ |
| 4 | 162 | 0.45 | 0.75 | 32 | MSJ |
Interfaces
3 interfaces between chains.
- A–B · 1683 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1674 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1661 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3ARN · Human dUTPase in complex with novel uracil derivative · the same entry in another collection · chain A against A, TM-score 1.00
- P33316 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P33316
- Elsewhere: RCSB PDB 3ARN · PDBe 3ARN · UniProt P33316
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