MolNFT v1 · #74689 · protein
Structure of the yeast dutpase DUT1 in complex with dumpnpp
3P48 · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “Structure of the yeast dutpase DUT1 in complex with dumpnpp”. X-ray diffraction, 2 ligands (DUP, MG), 4 pockets (best druggability 0.78). MolNFT v1 #74689 on GenesisL1: 3D…
- PDB
- 3P48
- Type
- protein
- Length
- 381 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
- P33317
- Ligands
- DUP, MG
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 46% strand | P33317 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 126 | 6% helix, 46% strand | P33317 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 128 | 5% helix, 46% strand | P33317 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.78 | 0.97 | 29 | empty |
| 2 | 195 | 0.51 | 0.77 | 26 | DUP, MG |
| 3 | 157 | 0.48 | 0.77 | 27 | DUP, MG |
| 4 | 148 | 0.48 | 0.77 | 27 | DUP, MG |
Interfaces
3 interfaces between chains.
- B–C · 1488 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1454 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1409 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3P48 · Structure of the yeast dUTPase DUT1 in complex with dUMPNPP · the same entry in another collection · chain A against A, TM-score 1.00
- P33317 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P33317
- Elsewhere: RCSB PDB 3P48 · PDBe 3P48 · UniProt P33317
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