Research workbench
The crystal structure of trypanosoma cruzi dutpase in complex with dudp
Analyse The crystal structure of trypanosoma cruzi dutpase in complex with dudp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OGK
- Type
- protein
- Length
- 946 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine triphosphatase
- EC
- 3.6.1.23
- UniProt
- O15923
- Ligands
- DUD
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 229 | 69% helix, 0% strand | O15923 |
| B | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 239 | 65% helix, 2% strand | O15923 |
| D | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 237 | 62% helix, 1% strand | O15923 |
| E | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 241 | 64% helix, 2% strand | O15923 |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 3 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.71 | 0.90 | 32 | DUD |
| 2 | 394 | 0.66 | 0.80 | 49 | DUD |
| 3 | 132 | 0.66 | 0.88 | 27 | DUD |
| 4 | 218 | 0.55 | 0.78 | 23 | empty |
| 5 | 93 | 0.50 | 0.82 | 18 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1914 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1655 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 817 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OGK · The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP · 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 O15923
- Elsewhere: RCSB PDB 1OGK · PDBe 1OGK · UniProt O15923
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.