Research workbench
Dictyostelium discoideum dutpase at 2.2 ångström
Analyse Dictyostelium discoideum dutpase at 2.2 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9K
- Type
- protein
- Length
- 386 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
- Q54BW5
- Ligands
- DUP, MG, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 128 | 5% helix, 45% strand | Q54BW5 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 130 | 5% helix, 42% strand | Q54BW5 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 5 copies · chains B, C, A
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.79 | 0.98 | 28 | MG |
| 2 | 142 | 0.46 | 0.77 | 27 | DUP |
| 3 | 136 | 0.43 | 0.76 | 29 | MG, DUP |
| 4 | 62 | 0.42 | 0.82 | 15 | empty |
| 5 | 56 | 0.34 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1574 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1557 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1550 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5F9K · Dictyostelium discoideum dUTPase at 2.2 Angstrom · the same entry in another collection · chain A against A, TM-score 1.00
- Q54BW5 · 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 Q54BW5
- Elsewhere: RCSB PDB 5F9K · PDBe 5F9K · UniProt Q54BW5
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