Research workbench
Crystal structure of LYSINE/ORNITHINE decarboxylase complexed with cadaverine from vibrio vulnificus
Analyse Crystal structure of LYSINE/ORNITHINE decarboxylase complexed with cadaverine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PLK
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSINE/ORNITHINE decarboxylase
- EC
- 4.1.1.18, 4.1.1.17
- UniProt
- Q8D594
- Ligands
- P3D
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18, 4.1.1.17) | protein | 370 | 36% helix, 25% strand | Q8D594 |
| B | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18, 4.1.1.17) | protein | 364 | 35% helix, 24% strand | Q8D594 |
Ligands and binding sites
- P3D · (4-{(E)-[(5-aminopentyl)imino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.69 | 0.84 | 47 | P3D |
| 2 | 283 | 0.67 | 0.82 | 52 | P3D |
| 3 | 154 | 0.56 | 0.81 | 34 | empty |
| 4 | 160 | 0.48 | 0.77 | 28 | empty |
| 5 | 123 | 0.47 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2566 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 2PLK · Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio… · 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 Q8D594
- Elsewhere: RCSB PDB 2PLK · PDBe 2PLK · UniProt Q8D594
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