Research workbench
The crystal structure of leishmania major dutpase in complex deoxyuridine
Analyse The crystal structure of leishmania major dutpase in complex deoxyuridine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YB0
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase
- EC
- 3.6.1.23
- UniProt
- O15826
- Ligands
- DUR, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutpase (EC 3.6.1.23) | protein | 258 | 64% helix, 3% strand | O15826 |
| B | Dutpase (EC 3.6.1.23) | protein | 263 | 62% helix, 3% strand | O15826 |
| D | Dutpase (EC 3.6.1.23) | protein | 255 | 62% helix, 3% strand | O15826 |
| E | Dutpase (EC 3.6.1.23) | protein | 264 | 60% helix, 2% strand | O15826 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · 4 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 9 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.82 | 0.90 | 66 | DUR, SO4 |
| 2 | 376 | 0.81 | 0.90 | 67 | DUR, SO4 |
| 3 | 557 | 0.74 | 0.82 | 71 | SO4 |
| 4 | 55 | 0.49 | 0.86 | 18 | empty |
| 5 | 174 | 0.48 | 0.76 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1804 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1801 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 969 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YB0 · The Crystal Structure of Leishmania major dUTPase in complex deoxyuridine · 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 O15826
- Elsewhere: RCSB PDB 2YB0 · PDBe 2YB0 · UniProt O15826
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