Research workbench
Crystal structure of trypanosoma brucei adometdc-DELTA26 monomer
Analyse Crystal structure of trypanosoma brucei adometdc-DELTA26 monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVO
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase proenzyme
- EC
- 4.1.1.50
- UniProt
- Q587A7
- Ligands
- PYR, NA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 254 | 26% helix, 37% strand | Q587A7 |
| B | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 59 | 22% helix, 37% strand | Q587A7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.79 | 0.84 | 90 | empty |
| 2 | 53 | 0.52 | 0.88 | 18 | PYR |
| 3 | 73 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2856 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5TVO · Crystal structure of Trypanosoma brucei AdoMetDC-delta26 monomer · 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 Q587A7
- Elsewhere: RCSB PDB 5TVO · PDBe 5TVO · UniProt Q587A7
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