MolNFT v1 · #47083 · protein
A structural insight into the inhibition of human and leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane
2OO0: “A structural insight into the inhibition of human and leishmania donovani ornithine decarboxylases by…”. X-ray diffraction, 3 ligands (PLP, XAP, N2P), 15 pockets (best druggability 0.78). MolNFT v1 #47083 on GenesisL1: 3D structure…
- PDB
- 2OO0
- Type
- protein
- Length
- 837 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- P11926
- Ligands
- PLP, XAP, N2P
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 419 | 39% helix, 23% strand | P11926 |
| B | Ornithine decarboxylase (EC 4.1.1.17) | protein | 418 | 38% helix, 23% strand | P11926 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- XAP · 3-aminooxy-1-aminopropane · ligand · 2 copies · chains A, B
- N2P · Pentane-1,5-diamine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.78 | 0.97 | 31 | PLP, XAP |
| 2 | 106 | 0.78 | 0.98 | 34 | PLP, XAP |
| 3 | 323 | 0.68 | 0.82 | 33 | N2P |
| 4 | 301 | 0.68 | 0.82 | 30 | N2P |
| 5 | 129 | 0.50 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2592 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2OO0 · A structural insight into the inhibition of human and Leishmania donovani ornithine… · the same entry in another collection · chain A against A, TM-score 1.00
- P11926 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P11926) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P11926
- Elsewhere: RCSB PDB 2OO0 · PDBe 2OO0 · UniProt P11926
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