Research workbench
Structure of leishmania donovani omp decarboxylase
Analyse Structure of leishmania donovani omp decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QW3
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine-5-phosphate DECARBOXYLASE/OROTATE phosphoribosyltransferase, putative…
- EC
- 2.4.2.10, 4.1.1.23
- UniProt
- A4HWV2
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine-5-phosphate DECARBOXYLASE/OROTATE phosphoribosyltransferase, putative (ompdcase-oprtase, putative) (EC 2.4.2.10, 4.1.1.23) | protein | 250 | 50% helix, 18% strand | A4HWV2 |
| B | Orotidine-5-phosphate DECARBOXYLASE/OROTATE phosphoribosyltransferase, putative (ompdcase-oprtase, putative) (EC 2.4.2.10, 4.1.1.23) | protein | 250 | 48% helix, 17% strand | A4HWV2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.81 | 0.98 | 23 | empty |
| 2 | 272 | 0.59 | 0.79 | 35 | SO4 |
| 3 | 187 | 0.54 | 0.79 | 29 | SO4 |
| 4 | 58 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2173 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 3QW3 · Structure of Leishmania donovani OMP decarboxylase · 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 A4HWV2
- Elsewhere: RCSB PDB 3QW3 · PDBe 3QW3 · UniProt A4HWV2
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