Research workbench
Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene AT5G11950
Analyse Ensemble refinement of the crystal structure of a lysine decarboxylase-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q4D
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine decarboxylase-like protein AT5G11950
- UniProt
- Q84MC2
- Ligands
- NO3
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine decarboxylase-like protein AT5G11950 | protein | 184 | 46% helix, 15% strand | Q84MC2 |
| B | Lysine decarboxylase-like protein AT5G11950 | protein | 181 | 50% helix, 14% strand | Q84MC2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.71 | 0.86 | 32 | EDO |
| 2 | 167 | 0.70 | 0.89 | 36 | empty |
| 3 | 60 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2010 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2Q4D · Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q84MC2 · AlphaFold monomer V2.0 prediction for cytokinin riboside 5'-monophosphate… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q84MC2
- Elsewhere: RCSB PDB 2Q4D · PDBe 2Q4D · UniProt Q84MC2
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