MolNFT v1 · #28412 · protein
X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene AT5G11950
1YDH: “X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene AT5G11950”. X-ray diffraction, 1 ligand (NO3), 2 pockets (best druggability 0.68). MolNFT v1 #28412 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1YDH
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT5G11950
- UniProt
- Q84MC2
- Ligands
- NO3
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AT5G11950 | protein | 184 | 49% helix, 18% strand | Q84MC2 |
| B | AT5G11950 | protein | 181 | 50% helix, 18% strand | Q84MC2 |
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 | 210 | 0.68 | 0.86 | 34 | EDO |
| 2 | 152 | 0.64 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2007 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1YDH · X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene… · 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 B 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 1YDH · PDBe 1YDH · UniProt Q84MC2
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