MolNFT v1 · #48186 · protein
Crystal structure of LYSINE/ORNITHINE decarboxylase complexed with putrescine from vibrio vulnificus
2PLJ: “Crystal structure of LYSINE/ORNITHINE decarboxylase complexed with putrescine from vibrio vulnificus”. X-ray diffraction, 2 ligands (P3T, MG), 8 pockets (best druggability 0.69). MolNFT v1 #48186 on GenesisL1: 3D structure, binding…
- PDB
- 2PLJ
- Type
- protein
- Length
- 739 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
- P3T, MG
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18, 4.1.1.17) | protein | 376 | 35% helix, 25% strand | Q8D594 |
| B | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18, 4.1.1.17) | protein | 363 | 36% helix, 24% strand | Q8D594 |
Ligands and binding sites
- P3T · (4-{[(4-aminobutyl)amino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.69 | 0.85 | 45 | P3T |
| 2 | 264 | 0.68 | 0.84 | 50 | P3T |
| 3 | 179 | 0.60 | 0.83 | 34 | empty |
| 4 | 135 | 0.48 | 0.79 | 32 | empty |
| 5 | 101 | 0.42 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2426 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2PLJ · Crystal structure of lysine/ornithine decarboxylase complexed with putrescine 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 2PLJ · PDBe 2PLJ · UniProt Q8D594
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