MolNFT v1 · #6147 · protein
Crystal structure of trypanosoma brucei ornithine decarboxylase (odc) complexed with putrescine, ODC'S reaction product.
1F3T: “Crystal structure of trypanosoma brucei ornithine decarboxylase (odc) complexed with putrescine, ODC'S…”. X-ray diffraction, 2 ligands (PLP, PUT), 20 pockets (best druggability 0.74). MolNFT v1 #6147 on GenesisL1: 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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