Research workbench
Crystal structure of trypanosoma brucei dutpase with dupnp, CA2+ and na+
Analyse Crystal structure of trypanosoma brucei dutpase with dupnp, CA2+ and na+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DK4
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine triphosphatase
- EC
- 3.6.1.23
- UniProt
- Q57ZH3
- Ligands
- DUN, CA, NA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 218 | 66% helix, 2% strand | Q57ZH3 |
| B | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 217 | 69% helix, 0% strand | Q57ZH3 |
Ligands and binding sites
- DUN · 2'-deoxyuridine 5'-alpha,beta-imido-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.75 | 0.94 | 28 | DUN, CA |
| 2 | 138 | 0.72 | 0.91 | 28 | DUN, CA, NA |
| 3 | 165 | 0.44 | 0.75 | 23 | NA |
| 4 | 70 | 0.33 | 0.76 | 13 | empty |
| 5 | 60 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1382 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4DK4 · Crystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ and Na+ · the same entry in another collection · 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 Q57ZH3
- Elsewhere: RCSB PDB 4DK4 · PDBe 4DK4 · UniProt Q57ZH3
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