Research workbench
Crystal structure of trypanosoma brucei ornithine decarboxylase (odc) complexed with putrescine, ODC'S reaction product.
Analyse Crystal structure of trypanosoma brucei ornithine decarboxylase (odc) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F3T
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- P07805
- Ligands
- PLP, PUT
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 378 | 36% helix, 23% strand | P07805 |
| B | Ornithine decarboxylase (EC 4.1.1.17) | protein | 381 | 36% helix, 23% strand | P07805 |
| C | Ornithine decarboxylase (EC 4.1.1.17) | protein | 370 | 35% helix, 24% strand | P07805 |
| D | Ornithine decarboxylase (EC 4.1.1.17) | protein | 367 | 36% helix, 24% strand | P07805 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- PUT · 1,4-diaminobutane · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.74 | 0.82 | 62 | PLP, PUT |
| 2 | 231 | 0.70 | 0.86 | 40 | PLP, PUT |
| 3 | 230 | 0.69 | 0.85 | 39 | PLP, PUT |
| 4 | 306 | 0.67 | 0.82 | 44 | PLP, PUT |
| 5 | 264 | 0.59 | 0.79 | 36 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2255 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2203 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1F3T · Crystal structure of trypanosoma brucei ornithine decarboxylase (odc) complexed 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 D 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 1F3T · PDBe 1F3T · UniProt P07805
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