MolNFT v1 · #55137 · protein
The crystal structure of leishmania major dutpase in complex dump
2YAZ: “The crystal structure of leishmania major dutpase in complex dump”. X-ray diffraction, 3 ligands (UMP, MG, SO4), 17 pockets (best druggability 0.79). MolNFT v1 #55137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YAZ
- Type
- protein
- Length
- 1,034 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
- UMP, MG, SO4
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Dutpase (EC 3.6.1.23) | protein | 257 | 64% helix, 3% strand | O15826 |
| B | Dutpase (EC 3.6.1.23) | protein | 263 | 59% helix, 2% strand | O15826 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 3 copies · chains A, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.79 | 0.89 | 67 | UMP, MG |
| 2 | 1104 | 0.79 | 0.80 | 126 | SO4, UMP, MG |
| 3 | 195 | 0.71 | 0.88 | 34 | UMP, MG |
| 4 | 99 | 0.52 | 0.83 | 20 | empty |
| 5 | 52 | 0.50 | 0.87 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1791 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1791 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 960 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YAZ · The Crystal Structure of Leishmania major dUTPase in complex dUMP · the same entry in another collection · chain B against B, 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 2YAZ · PDBe 2YAZ · UniProt O15826
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