Research workbench
Ornithine decarboxylase from trypanosoma brucei K69A mutant in complex with alpha-difluoromethylornithine
Analyse Ornithine decarboxylase from trypanosoma brucei K69A mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2TOD
- Type
- protein
- Length
- 1,411 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Trypanosoma brucei
- Molecule
- Protein (ornithine decarboxylase)
- EC
- 4.1.1.17
- UniProt
- P07805
- Ligands
- DMO, PLP
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Protein (ornithine decarboxylase) (EC 4.1.1.17) | protein | 353 | 35% helix, 24% strand | P07805 |
| B | Protein (ornithine decarboxylase) (EC 4.1.1.17) | protein | 352 | 35% helix, 24% strand | P07805 |
Ligands and binding sites
- DMO · Alpha-difluoromethylornithine · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.76 | 0.83 | 71 | DMO, PLP |
| 2 | 537 | 0.75 | 0.83 | 70 | DMO, PLP |
| 3 | 294 | 0.72 | 0.86 | 48 | PLP, DMO |
| 4 | 268 | 0.71 | 0.86 | 40 | PLP, DMO |
| 5 | 276 | 0.60 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2230 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2219 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2TOD · Ornithine decarboxylase from trypanosoma brucei K69A mutant in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P07805 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P07805) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P07805
- Elsewhere: RCSB PDB 2TOD · PDBe 2TOD · UniProt P07805
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