Research workbench
Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene AT2G37210
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
- 2Q4O
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein AT2G37210/T2N18.3
- UniProt
- Q8L8B8
- Ligands
- MG, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein AT2G37210/T2N18.3 | protein | 175 | 47% helix, 18% strand | Q8L8B8 |
| B | Uncharacterized protein AT2G37210/T2N18.3 | protein | 173 | 48% helix, 18% strand | Q8L8B8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.55 | 0.78 | 31 | SO4 |
| 2 | 155 | 0.51 | 0.79 | 30 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1885 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2Q4O · 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
- Q8L8B8 · 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 Q8L8B8
- Elsewhere: RCSB PDB 2Q4O · PDBe 2Q4O · UniProt Q8L8B8
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