Research workbench
Crystal structure of lysine decarboxylase from selenomonas ruminantium in C2 space group
Analyse Crystal structure of lysine decarboxylase from selenomonas ruminantium in C2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GJM
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSINE/ORNITHINE decarboxylase
- EC
- 4.1.1.18
- UniProt
- O50657
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18) | protein | 381 | 35% helix, 22% strand | O50657 |
| B | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18) | protein | 368 | 37% helix, 22% strand | O50657 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.73 | 0.83 | 53 | empty |
| 2 | 456 | 0.67 | 0.79 | 45 | empty |
| 3 | 78 | 0.66 | 0.92 | 27 | empty |
| 4 | 57 | 0.64 | 0.94 | 29 | empty |
| 5 | 379 | 0.60 | 0.76 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 2539 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5GJM · Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in C2 space group · the same entry in another collection · chain A against A, TM-score 1.00
- O50657 · AlphaFold monomer V2.0 prediction for LYSINE/ORNITHINE decarboxylase (O50657) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O50657
- Elsewhere: RCSB PDB 5GJM · PDBe 5GJM · UniProt O50657
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