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Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418
Analyse Crystal structure determination of T. brucei ornithine decarboxylase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NJJ
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- Q9TZZ6
- Ligands
- ORX, GET
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 349 | 34% helix, 25% strand | Q9TZZ6 |
| B | Ornithine decarboxylase (EC 4.1.1.17) | protein | 349 | 35% helix, 25% strand | Q9TZZ6 |
| C | Ornithine decarboxylase (EC 4.1.1.17) | protein | 352 | 35% helix, 24% strand | Q9TZZ6 |
| D | Ornithine decarboxylase (EC 4.1.1.17) | protein | 354 | 36% helix, 25% strand | Q9TZZ6 |
Ligands and binding sites
- ORX · N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-ornithine · ligand · 4 copies · chains A, B, C, D
- GET · Geneticin · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.71 | 0.80 | 64 | ORX |
| 2 | 598 | 0.71 | 0.79 | 74 | ORX |
| 3 | 539 | 0.70 | 0.80 | 65 | ORX |
| 4 | 500 | 0.69 | 0.79 | 70 | ORX |
| 5 | 297 | 0.62 | 0.79 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1629 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1616 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1NJJ · Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine… · 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 Q9TZZ6
- Elsewhere: RCSB PDB 1NJJ · PDBe 1NJJ · UniProt Q9TZZ6
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